@article {pmid40743118,
year = {2025},
author = {Ozturk, S and Ekmen, FG and Ekmen, H and Ünal, EM and Er, A and Keskin, E and Arbuckle, BS},
title = {Decoding past microbial life and antibiotic resistance in İnonü Cave's archaeological soil.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0326358},
doi = {10.1371/journal.pone.0326358},
pmid = {40743118},
issn = {1932-6203},
mesh = {*Soil Microbiology ; *Archaeology ; *Bacteria/genetics/classification/drug effects ; *Caves/microbiology ; RNA, Ribosomal, 16S/genetics ; Humans ; *Drug Resistance, Microbial/genetics ; Microbiota/genetics ; Turkey ; },
abstract = {This study, which bridges the disciplines of archaeology and microbiology, examines the ancient bacterial communities and antibiotic-resistance genes in soil samples collected from İnönü Cave in Zonguldak, Turkiye. Our aim is to provide a comprehensive understanding of historical human activities and their influence on microbial communities. Soil samples were gathered from four distinct cultural levels from the Chalcolithic Age to the Early Iron Age. The microbial communities were characterized, and antibiotic-resistance genes were identified using high-throughput sequencing of 16S rRNA genes and metagenomic studies. This interdisciplinary approach not only enriches our understanding of ancient microbial communities but also opens up new avenues for research and collaboration. The results of our study showed a wide range of microorganisms, including prominent bacterial groups such as Acidobacteriota, Actinobacteriota, Bacteroidota, Chloroflexi, Cyanobacteria, Firmicutes, Myxococcota, and Proteobacteria. The study identified the presence of the tetracycline resistance gene tetA in Chalcolithic samples, the class 1 integron intl1 in Early Bronze Age samples, and the oxacillinase gene OXA58 in Late Bronze Age samples. These findings underscore the long-term impact of human activities on microbial communities, as antibiotic-resistance genes have been present and have remained over various historical periods, perhaps influenced by both human activities and environmental variables. This knowledge is crucial for understanding the resilience and adaptability of microbial communities in the face of human-induced changes. The coexistence of these resistance genes and alterations in the microbial population suggest substantial connections between human activities and soil microbiota. This study, which draws on the fields of archaeology, microbiology, and environmental science, offers valuable insights into the ancient microbial ecology and underscores the enduring presence of antibiotic resistance. It emphasizes the necessity of a comprehensive, interdisciplinary approach, spanning multiple fields, to comprehend microbial communities' evolution and resistance mechanisms in archaeological settings.},
}

*Soil Microbiology
*Archaeology
*Bacteria/genetics/classification/drug effects
*Caves/microbiology
RNA, Ribosomal, 16S/genetics
Humans
*Drug Resistance, Microbial/genetics
Microbiota/genetics
Turkey

@article {pmid40742122,
year = {2025},
author = {Wu, H and Jiang, X and Xi, Y and Ning, S and Wu, H and Xin, W and Peng, W and Wang, S and Zhang, W},
title = {Genetic characterization of the marmot gut virome in high-altitude Qinghai Province and identification of novel viruses with zoonotic potential.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0029725},
doi = {10.1128/msphere.00297-25},
pmid = {40742122},
issn = {2379-5042},
abstract = {The high-altitude ecosystems of Qinghai Province, China, harbor unique viral communities shaped by extreme environmental conditions and host adaptations. This study presents a comprehensive genetic characterization of the marmot gut virome, revealing novel viral strains with zoonotic potential. Using viral metagenomics, we analyzed intestinal contents from 70 marmots collected from Chengduo and Maqin counties. Sequencing on the Illumina NovaSeq 6000 platform identified 19 viral genomes belonging to four major families: Adenoviridae, Astroviridae, Parvoviridae, and Picornaviridae, along with four novel circular Rep-encoding single-stranded DNA (CRESS DNA) viruses. Phylogenetic analyses demonstrated close relationships between marmot-derived strains and viruses from humans, bats, and other mammals, highlighting potential cross-species transmission risks. Notably, bat-associated adenoviruses showed closer phylogenetic proximity to human strains, while novel parvoviruses formed a distinct clade within the Dependoparvovirus genus. The discovery of a novel astrovirus with low sequence similarity to known genera underscores the need for taxonomic reclassification. Additionally, a novel picornavirus related to Sapelovirus and four divergent CRESS DNA viruses were identified, expanding our understanding of viral diversity in high-altitude rodents. These findings emphasize the role of marmots as viral reservoirs and highlight the importance of high-altitude ecosystems as hotspots for zoonotic pathogen emergence. This study provides critical insights into viral evolution, host adaptation, and zoonotic risks, advocating for integrated surveillance strategies to mitigate future spillover events.IMPORTANCEViruses are the most abundant and diverse biological entities on Earth, yet their presence in wildlife from extreme environments remains poorly understood. High-altitude ecosystems, shaped by harsh conditions like intense UV radiation and low oxygen levels, create unique settings for virus evolution. This study is the first to comprehensively profile the gut virome of marmots in Qinghai Province, uncovering novel viral strains and highlighting how extreme environments drive viral diversity. Marmots, as key species in these regions, can act as bridges for virus transmission among wildlife, livestock, and humans, posing zoonotic risks. Understanding these viral communities is essential for predicting and preventing future outbreaks. Our findings emphasize the urgent need for integrated, One Health-based surveillance strategies to safeguard both public health and biodiversity in fragile high-altitude ecosystems.},
}

@article {pmid40739184,
year = {2025},
author = {Tang, HB and Si, YX and Li, HD and Dang, W and Lu, HL},
title = {Intestinal microbial dysbiosis under nitrite stress in juvenile three-keeled pond turtles, Mauremys reevesii.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {466},
doi = {10.1186/s12866-025-04198-8},
pmid = {40739184},
issn = {1471-2180},
support = {32471577//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Turtles/microbiology ; *Nitrites/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Dysbiosis/microbiology/veterinary/chemically induced ; *Bacteria/classification/genetics/drug effects/isolation & purification ; Stress, Physiological ; Intestines/microbiology ; *Water Pollutants, Chemical/toxicity ; Aquaculture ; },
abstract = {BACKGROUND: Nitrite is one of the primary pollutants in high-density aquaculture systems, and may cause various toxic effects (e.g., oxidative damage, metabolic and immune dysregulation, histological inflammation, etc.) on economically important aquaculture species, such as echinoderms, crustaceans and fish. Nitrite can also disrupt the intestinal function and microbiota in some fish and amphibians. However, intestinal physiological and microbial responses of cultured turtles under nitrite stress were rarely explored.

METHOD: Twenty Mauremys reevesii juveniles were exposed to different nitrite levels and fed with a commercial diet. Their intestinal content samples were analyzed for microbial diversity and composition.

RESULTS: Nitrite exposure reduced intestinal microbial diversity, with lower α-diversity values in higher-concentration exposed turtles. It also changed the microbial composition. After exposure, the abundances of Bacteroidetes and Firmicutes decreased, but that of Proteobacteria increased at the phylum level. Similarly, abundances of some potentially beneficial bacterial genera, e.g., Prevotella_1, Christensenellaceae_R-7, Muribaculaceae_ge, were shown to decrease, but those of putatively pathogenic genera, e.g., Halomonas, Nesterenkonia, increased at the genus level. Furtherly, potentially altered metabolic pathways (e.g., biosynthesis of ansamycins and vancomycin group antibiotics) were revealed by functional predictions of intestinal microbiota.

CONCLUSION: This study highlighted intestinal microbial dysbiosis and prevalence of putatively pathogenic bacteria in cultured turtles under nitrite stress. Excessive levels of nitrite would alter the health status of aquatic animals by disrupting their intestinal microbiome.},
}

Animals
*Turtles/microbiology
*Nitrites/toxicity
*Gastrointestinal Microbiome/drug effects
*Dysbiosis/microbiology/veterinary/chemically induced
*Bacteria/classification/genetics/drug effects/isolation & purification
Stress, Physiological
Intestines/microbiology
*Water Pollutants, Chemical/toxicity
Aquaculture

@article {pmid40739125,
year = {2025},
author = {Jiang, W and Xiong, M and Feng, S and Liu, Q and Chen, Y and Zou, S and Kang, D},
title = {Water content alters soil organic carbon metabolism via microbial traits in Tibetan alpine peatlands.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {27793},
doi = {10.1038/s41598-025-13788-5},
pmid = {40739125},
issn = {2045-2322},
support = {No. 2023NSFSC0143//the Natural Science Foundation of Sichuan Provence/ ; No. 31800458//the National Natural Science Foundation of China/ ; No. 2019-ZL-19//Sichuan Province Transportation Science and Technology Project: Research and Demonstration on Crucial Technologies of Wetland Eco-environment Protection Under the Influence of Highway Engineering on the Western Sichuan Plateau/ ; },
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Carbon/metabolism ; Tibet ; *Water/analysis ; Carbon Cycle ; Archaea/metabolism/genetics ; Bacteria/metabolism/genetics ; Fungi/metabolism/genetics ; Microbiota ; },
abstract = {Alpine peatlands on the eastern Tibetan Plateau are vital carbon sinks, with soil moisture playing a key role in peatland carbon cycling. However, they face disruptions in their carbon balance due to drought, which reduces soil water content. Therefore, this study investigated microbially driven water-carbon interactions through field surveys, laboratory incubations, and metagenomics. Soil drying contributes to changes in both the metabolic quotient (qCO2) and the microbial quotient (Cmic: Corg), as well as the microbial abundance. As the soil water content decreased, both qCO2 and Cmic: Corg exhibited an overall increasing trend. Moreover, soil water content had a more significant effect on soil bacteria, while its effect on fungi and archaea was minimal. Soil microbial carbon decomposition genes were also influenced by changes in soil water content. Next, we used RDA to analyze the relationship between soil respiration quotient values and microbial traits. The results revealed that Actinobacteria were strongly negatively correlated with qCO2, whereas Archaea and Candidatus_R were positively correlated with qCO2. Additionally, Cmic: Corg was closely linked to fungi, and both Proteobacteria and Acidobacteria exhibited positive correlations. qCO2 had a strong negative correlation with genes involved in the degradation of monosaccharides and hemicellulose, whereas Cmic: Corg was positively correlated with genes related to the degradation of cellulose and lignin. Moreover, droughts affected microbial residue carbon and associated carbon metabolic pathways. Therefore, changes in soil water content may be an important factor influencing carbon metabolism processes in peatlands. This study deepens our understanding of the effects of drought on soil metabolism and microbial dynamics in alpine peatlands and provides new insights into the microecological mechanisms of soil carbon cycling in these ecosystems in the context of global change.},
}

*Soil Microbiology
*Soil/chemistry
*Carbon/metabolism
Tibet
*Water/analysis
Carbon Cycle
Archaea/metabolism/genetics
Bacteria/metabolism/genetics
Fungi/metabolism/genetics
Microbiota

@article {pmid40541587,
year = {2025},
author = {Pletsch, EA and Smith, AD and Ragonese, JS and Narrowe, AB and Cheung, L and Chen, CT and Wang, TT and Dawson, HD},
title = {Broccoli Consumption Alters Microbial Diversity, Metatranscriptome, and Host Transcriptome in Mice Fed a Total Western Diet.},
journal = {The Journal of nutrition},
volume = {155},
number = {8},
pages = {2545-2559},
doi = {10.1016/j.tjnut.2025.05.041},
pmid = {40541587},
issn = {1541-6100},
mesh = {Animals ; *Brassica ; Male ; Mice, Inbred C57BL ; *Gastrointestinal Microbiome/drug effects ; *Diet, Western ; *Transcriptome ; Mice ; Cecum/microbiology ; },
abstract = {BACKGROUND: Cruciferous vegetables (CVs) are a source of dietary fiber and phytochemicals that alter the microbiome in animals and humans. Constituent cruciferous vegetable compounds, such as glucosinolates, have demonstrated anti-inflammatory properties in animal models, though often using doses and basal diets that are not relevant to humans. The mechanism(s) is unclear, but the gut microbiota may metabolize these compounds into bioactive molecules that influence immune pathways.

OBJECTIVES: We investigated the effects of broccoli powder (BP)-supplemented total Western diet (TWD) on changes in the gut microbiome, the host transcriptome, and the metatranscriptome at levels relevant to the human diet to understand how these changes affect metabolic and immune functions.

METHODS: C57BL/6 male mice (n = 40) were fed a TWD control diet for 6 wk followed by supplementation with 0%, 0.5%, 1%, or 2.5% BP (reflecting a human intake from ¼-1 cup/d) for 3 wk. Microbial communities from cecal contents were taxonomically profiled using 16S ribosomal ribonucleic acid amplicon and shotgun metagenomic sequencing, and metatranscriptomics was used to assess the functionality of the microbial communities. The host cecal transcriptome was also assessed.

RESULTS: β-diversity was significantly higher (P = 1.20 × 10[-3]) for mice fed the 2.5% BP diet compared to the control group at the species level. Lachnospiraceae MD335 was significantly more abundant in mice fed higher levels of broccoli, and analysis of bacterial ribonucleic acid transcripts indicated a dose-dependent increase in transcription of genes associated with butyrate and acetate production, plant cell wall degradation, and carbohydrate utilization. Activation of the aryl hydrocarbon receptor pathway in the cecum was evident.

CONCLUSIONS: Consumption of a broccoli-supplemented TWD induces changes in the gut microbiome, host, and microbial gene expression that affect immune health and inflammation in the gut at levels that are achievable in the human diet.},
}

Animals
*Brassica
Male
Mice, Inbred C57BL
*Gastrointestinal Microbiome/drug effects
*Diet, Western
*Transcriptome
Mice
Cecum/microbiology

@article {pmid30040657,
year = {2019},
author = {Wassan, JT and Wang, H and Browne, F and Zheng, H},
title = {A Comprehensive Study on Predicting Functional Role of Metagenomes Using Machine Learning Methods.},
journal = {IEEE/ACM transactions on computational biology and bioinformatics},
volume = {16},
number = {3},
pages = {751-763},
doi = {10.1109/TCBB.2018.2858808},
pmid = {30040657},
issn = {1557-9964},
mesh = {*Machine Learning ; *Metagenomics/methods ; Humans ; *Metagenome/genetics ; *Microbiota/genetics ; Algorithms ; ROC Curve ; },
abstract = {"Metagenomics" is the study of genomic sequences obtained directly from environmental microbial communities with the aim to linking their structures with functional roles. The field has been aided in the unprecedented advancement through high-throughput omics data sequencing. The outcome of sequencing are biologically rich data sets. Metagenomic data consisting of microbial species which outnumber microbial samples, lead to the "curse of dimensionality" in datasets. Hence, the focus in metagenomics studies has moved towards developing efficient computational models using Machine Learning (ML), reducing the computational cost. In this paper, we comprehensively assessed various ML approaches to classifying high-dimensional human microbiota effectively into their functional phenotypes. We propose the application of embedded feature selection methods, namely, Extreme Gradient Boosting and Penalized Logistic Regression to determine important microbial species. The resultant feature set enhanced the performance of one of the most popular state-of-the-art methods, Random Forest (RF) over metagenomic studies. Experimental results indicate that the proposed method achieved best results in terms of accuracy, area under the Receiver Operating Characteristic curve (ROC-AUC), and major improvement in processing time. It outperformed other feature selection methods of filters or wrappers over RF and classifiers such as Support Vector Machine (SVM), Extreme Learning Machine (ELM), and k- Nearest Neighbors (k-NN).},
}

*Machine Learning
*Metagenomics/methods
Humans
*Metagenome/genetics
*Microbiota/genetics
Algorithms
ROC Curve

@article {pmid40736894,
year = {2025},
author = {Child, HT and Barber, DG and Maneein, S and Clayton, J and Love, J and Tennant, RK},
title = {Laboratory and In-Field Metagenomics for Environmental Monitoring.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2955},
number = {},
pages = {71-88},
doi = {10.1007/978-1-0716-4702-8_5},
pmid = {40736894},
issn = {1940-6029},
mesh = {*Metagenomics/methods ; *Environmental Monitoring/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Gene Library ; },
abstract = {Direct sequencing of DNA from environmental samples (eDNA) is increasingly utilized to provide a census of natural and industrial habitats. The methodology required to perform metagenomics can be divided into three distinct stages: DNA Purification, Library Preparation and Sequencing, and Bioinformatic Analysis. Here we demonstrate an end-to-end protocol that can be utilized either in the field or laboratory for metagenomic analysis of environmental samples utilizing the Oxford Nanopore Technologies MinION sequencing platform.},
}

*Metagenomics/methods
*Environmental Monitoring/methods
High-Throughput Nucleotide Sequencing/methods
Sequence Analysis, DNA/methods
Computational Biology/methods
Gene Library

@article {pmid40736175,
year = {2025},
author = {Shi, Q and Wei, Z and Pang, J and Qudsi, AI and Wei, M and Zhang, Z and Zhang, Y and Wang, Z and Chen, K and Xu, X and Lu, X and Liang, Q},
title = {Achromobacter in the Conjunctival Sac Microbiota: Potential Association With Acanthamoeba Keratitis Related to Orthokeratology Lenses.},
journal = {Investigative ophthalmology & visual science},
volume = {66},
number = {9},
pages = {71},
doi = {10.1167/iovs.66.9.71},
pmid = {40736175},
issn = {1552-5783},
mesh = {Humans ; Male ; Female ; *Microbiota ; *Acanthamoeba Keratitis/microbiology/etiology ; *Conjunctiva/microbiology ; Adult ; *Achromobacter/isolation & purification/genetics/physiology ; In Situ Hybridization, Fluorescence ; RNA, Ribosomal, 16S/genetics ; *Orthokeratologic Procedures/adverse effects/instrumentation ; Acanthamoeba ; *Contact Lenses/adverse effects ; Young Adult ; DNA, Bacterial/genetics/analysis ; Dysbiosis/microbiology ; Middle Aged ; },
abstract = {PURPOSE: Acanthamoeba keratitis (AK) is a severe infection linked to orthokeratology lens use, whereas the involvement of conjunctival microbiota in AK remains poorly understood. This study investigates microbiota dysbiosis in AK pathogenesis to inform microbiota-based interventions.

METHODS: Conjunctival swabs from 14 patients with AK and 10 healthy controls underwent 16S rRNA sequencing. Microbiome analysis compared diversity, taxa, and metabolic pathways. Functional assays quantified Achromobacter-enhanced Acanthamoeba adhesion and migration. Metagenomics and fluorescence in situ hybridization (FISH) with species-specific probes confirmed endosymbiosis.

RESULTS: Patients with AK showed reduced bacterial diversity compared with the healthy controls (P < 0.001) but similar richness. Relative abundance of Achromobacter in the AK group was higher compared to the healthy control group (P < 0.001). Achromobacter dominated microbiota among the AK group, being identified as a key biomarker via the linear discriminant analysis effect size (LEfSe). In vitro, Achromobacter increased Acanthamoeba adhesion (P = 0.007) and the migration area (P < 0.05). Metagenomic analysis and FISH further showed Achromobacter spp. as potential endosymbionts of Acanthamoeba. Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed upregulated phenylalanine, fatty acid, and propanoate metabolism in the AK group (all P < 0.001). MetaCyc highlighted enriched pyruvate fermentation to isobutanol, aerobic respiration I, and L-isoleucine biosynthesis II in the AK group (P < 0.001).

CONCLUSIONS: AK-associated conjunctival dysbiosis features Achromobacter dominance, reduced diversity, and altered metabolism. Achromobacter is associated with enhanced adhesion and migration of Acanthamoeba, indicating a possible symbiotic interaction and its potential as a biomarker and therapeutic target.},
}

Humans
Male
Female
*Microbiota
*Acanthamoeba Keratitis/microbiology/etiology
*Conjunctiva/microbiology
Adult
*Achromobacter/isolation & purification/genetics/physiology
In Situ Hybridization, Fluorescence
RNA, Ribosomal, 16S/genetics
*Orthokeratologic Procedures/adverse effects/instrumentation
Acanthamoeba
*Contact Lenses/adverse effects
Young Adult
DNA, Bacterial/genetics/analysis
Dysbiosis/microbiology
Middle Aged

@article {pmid40732945,
year = {2025},
author = {Kulecka, M and Jaworski, P and Zeber-Lubecka, N and Bałabas, A and Piątkowska, M and Czarnowski, P and Frączek, B and Tarnowski, W and Mikula, M and Ostrowski, J},
title = {The Gut Microbiome Obesity Index: A New Analytical Tool in the Metagenomics Workflow for the Evaluation of Gut Dysbiosis in Obese Humans.},
journal = {Nutrients},
volume = {17},
number = {14},
pages = {},
doi = {10.3390/nu17142320},
pmid = {40732945},
issn = {2072-6643},
support = {2018/29/B/NZ7/00809//National Science Center/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Obesity/microbiology ; Male ; Female ; *Metagenomics/methods ; Adult ; Feces/microbiology ; *Dysbiosis/microbiology/diagnosis ; Body Mass Index ; Middle Aged ; Bacteria/classification/genetics ; Workflow ; Case-Control Studies ; Young Adult ; },
abstract = {Background/Objectives: Our aim was to create a new method for analyzing metagenomics data, named the gut microbiome obesity index, using a set of taxa/biological functions that correlated with BMI. Methods: A total of 109 obese patients (73 women and 36 men, median BMI 43.0 kg/m[2]), 87 healthy control (HC) individuals (39 females and 48 males, median BMI 22.7 kg/m[2]), and 109 esports players (five females and 104 males, median BMI 23.0 kg/m[2]) were included in the study. To conduct metagenomic and metabolomic analyses, DNA and selected metabolites were isolated from fecal samples and used for whole-genome shotgun sequencing and gas chromatography/mass spectrometry, respectively. Results: Compared with HCs and esports players, obese patients with a BMI > 40 kg/m[2] had a significantly higher alpha diversity, as analyzed by the Shannon index, and significant dissimilarities in beta diversity. Both richness and diversity measures were correlated with BMI. Compared with HCs and esports players, 12 differential bacteria were found in the overall obesity group and 42 were found in those with a BMI > 40 kg/m[2]. Most of the altered species belonged to the Lachnospiraceae family. When the logarithmic relationship of the sums of the bacteria correlated with BMI was calculated to establish a taxonomic health index, it better differentiated between the obesity groups than a standard analytical pipeline; however, it did not differentiate between the HC and the BMI < 35 kg/m[2] obesity group. Therefore, we created a functional index based on BMI-associated biological pathways, which differentiated between all obesity groups. Conclusions: Of the obesity indices used to distinguish between healthy and obese microbiota analyzed in this study, a function-based index was more useful than a taxonomy-based index. We believe that gut microbiome indexes could be useful as part of routine metagenomics evaluations. However, an index developed in one geographical area might not be applicable to individuals in a different region and, therefore, further studies should develop separate indices for different populations or geographical regions rather than relying on a single index.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Obesity/microbiology
Male
Female
*Metagenomics/methods
Adult
Feces/microbiology
*Dysbiosis/microbiology/diagnosis
Body Mass Index
Middle Aged
Bacteria/classification/genetics
Workflow
Case-Control Studies
Young Adult

@article {pmid40731978,
year = {2025},
author = {Garcia, M and Bruna, P and Duran, P and Abanto, M},
title = {Cyanobacteria and Soil Restoration: Bridging Molecular Insights with Practical Solutions.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071468},
pmid = {40731978},
issn = {2076-2607},
abstract = {Soil degradation has been accelerating globally due to climate change, which threatens food production, biodiversity, and ecosystem balance. Traditional soil restoration strategies are often expensive, slow, or unsustainable in the long term. In this context, cyanobacteria have emerged as promising biotechnological alternatives, being the only prokaryotes capable of performing oxygenic photosynthesis. Moreover, they can capture atmospheric carbon and nitrogen, release exopolysaccharides (EPSs) that stabilize the soil, and facilitate the development of biological soil crusts (biocrusts). In recent years, the convergence of multi-omics tools, such as metagenomics, metatranscriptomics, and metabolomics, has advanced our understanding of cyanobacterial dynamics, their metabolic potential, and symbiotic interactions with microbial consortia, as exemplified by the cyanosphere of Microcoleus vaginatus. In addition, recent advances in bioinformatics have enabled high-resolution taxonomic and functional profiling of environmental samples, facilitating the identification and prediction of resilient microorganisms suited to challenging degraded soils. These tools also allow for the prediction of biosynthetic gene clusters and the detection of prophages or cyanophages within microbiomes, offering a novel approach to enhance carbon sequestration in dry and nutrient-poor soils. This review synthesizes the latest findings and proposes a roadmap for the translation of molecular-level knowledge into scalable biotechnological strategies for soil restoration. We discuss approaches ranging from the use of native biocrust strains to the exploration of cyanophages with the potential to enhance cyanobacterial photosynthetic activity. By bridging ecological functions with cutting-edge omics technologies, this study highlights the critical role of cyanobacteria as a nature-based solution for climate-smart soil management in degraded and arid ecosystems.},
}

@article {pmid40731321,
year = {2025},
author = {Rech de Laval, V and Dainat, B and Engel, P and Robinson-Rechavi, M},
title = {The BeeBiome data portal provides easy access to bee microbiome information.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {198},
pmid = {40731321},
issn = {1471-2105},
mesh = {Bees/microbiology ; Animals ; *Microbiota/genetics ; Metagenomics/methods ; *Databases, Genetic ; Metagenome ; },
abstract = {Bees can be colonized by a large diversity of microbes, including beneficial gut symbionts and detrimental pathogens, with implications for bee health. Over the last few years, researchers around the world have collected a huge amount of genomic and transcriptomic data about the composition, genomic content, and gene expression of bee-associated microbial communities. While each of these datasets by itself has provided important insights, the integration of such datasets provides an unprecedented opportunity to obtain a global picture of the microbes associated with bees and their link to bee health. The challenge of such an approach is that datasets are difficult to find within large generalist repositories and are often not readily accessible, which hinders integrative analyses. Here we present a publicly-available online resource, the BeeBiome data portal (https://www.beebiome.org), which provides an overview of and easy access to currently available metagenomic datasets involving bee-associated microbes. Currently the data portal contains 33,678 Sequence Read Archive (SRA) experiments for 278 Apoidea hosts. We present the content and functionalities of this portal. By providing access to all bee microbiomes in a single place, with easy filtering on relevant criteria, BeeBiome will allow faster progress of applied and fundamental research on bee biology and health. It should be a useful tool for researchers, academics, funding agencies, and governments, with beneficial impacts for stakeholders.},
}

Bees/microbiology
Animals
*Microbiota/genetics
Metagenomics/methods
*Databases, Genetic
Metagenome

@article {pmid40731267,
year = {2025},
author = {Xu, X and Qin, D and Qin, X and Gao, X and Li, C and Liu, X and Wu, G},
title = {Sustainable management of soil-borne disease: integrating fumigation with Andrographis paniculata residues to rebuild rhizosphere function.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {460},
doi = {10.1186/s12866-025-04188-w},
pmid = {40731267},
issn = {1471-2180},
support = {32060639//the National Natural Science Foundation of China/ ; 202105AC160037, 202205AC160077//the Reserve Talents Project for Yunnan Young and Middle-aged Academic and Technical Leaders/ ; },
mesh = {*Rhizosphere ; *Soil Microbiology ; *Fumigation/methods ; *Andrographis/chemistry ; *Plant Diseases/microbiology/prevention & control ; *Plant Extracts/pharmacology/chemistry ; Metabolomics ; Fusarium/drug effects ; Soil/chemistry ; Microbiota/drug effects ; Metagenomics ; },
abstract = {Continuous pepper cropping induces soil-borne diseases and disrupts rhizosphere microecological balance. This study employed untargeted metabolomics and metagenomics to investigate treatment effects on rhizosphere metabolic reprogramming and microbe-metabolite interactions. Aqueous and ethanolic extracts of Andrographis paniculata residues (TCMR) were rich in flavonoids, terpenoids, and phenolic acids, exhibiting significant inhibition against soil-borne pathogens (Fusarium oxysporum, Fusarium solani, and others; >70% inhibition at high doses). While single fumigation (W1, M1) transiently suppressed pathogens, it disrupted rhizosphere metabolic homeostasis. In contrast, combined fumigation-TCMR treatments (WC, MC) enhanced plant stress resistance, stabilized membrane integrity, and reshaped microbial communities by modulating amino acid, lipid, and phenylpropanoid biosynthesis pathways. Microbe-metabolite network analysis revealed that coupling carbon-nitrogen cycling with redox homeostasis drives soil microecological optimization. This integrated strategy provides a sustainable solution for continuous cropping obstacles through synergistic metabolic reprogramming and microbiome reconstruction.},
}

*Rhizosphere
*Soil Microbiology
*Fumigation/methods
*Andrographis/chemistry
*Plant Diseases/microbiology/prevention & control
*Plant Extracts/pharmacology/chemistry
Metabolomics
Fusarium/drug effects
Soil/chemistry
Microbiota/drug effects
Metagenomics

@article {pmid40730965,
year = {2025},
author = {Clark-Boucher, D and Coull, BA and Reeder, HT and Wang, F and Sun, Q and Starr, JR and Lee, KH},
title = {Group-wise normalization in differential abundance analysis of microbiome samples.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {196},
pmid = {40730965},
issn = {1471-2105},
support = {T32GM135117/GM/NIGMS NIH HHS/United States ; R01GM126257/GM/NIGMS NIH HHS/United States ; R01GM126257/GM/NIGMS NIH HHS/United States ; P30ES000002/ES/NIEHS NIH HHS/United States ; R03DE027486/DE/NIDCR NIH HHS/United States ; R03DE027486/DE/NIDCR NIH HHS/United States ; },
mesh = {*Microbiota/genetics ; Metagenome ; Algorithms ; *Metagenomics/methods ; Humans ; },
abstract = {BACKGROUND: A key challenge in differential abundance analysis (DAA) of microbial sequencing data is that the counts for each sample are compositional, resulting in potentially biased comparisons of the absolute abundance across study groups. Normalization-based DAA methods rely on external normalization factors that account for compositionality by standardizing the counts onto a common numerical scale. However, existing normalization methods have struggled to maintain the false discovery rate in settings where the variance or compositional bias is large. This article proposes a novel framework for normalization that can reduce bias in DAA by re-conceptualizing normalization as a group-level task. We present two new normalization methods within the group-wise framework: group-wise relative log expression (G-RLE) and fold-truncated sum scaling (FTSS).

RESULTS: G-RLE and FTSS achieve higher statistical power for identifying differentially abundant taxa than existing methods in model-based and synthetic data simulation settings. The two novel methods also maintain the false discovery rate in challenging scenarios where existing methods suffer. The best results are obtained from using FTSS normalization with the DAA method MetagenomeSeq.

CONCLUSION: Compared with other methods for normalizing compositional sequence count data prior to DAA, the proposed group-level normalization frameworks offer more robust statistical inference. With a solid mathematical foundation, validated performance in numerical studies, and publicly available software, these new methods can help improve rigor and reproducibility in microbiome research.},
}

*Microbiota/genetics
Metagenome
Algorithms
*Metagenomics/methods
Humans

@article {pmid40730483,
year = {2025},
author = {Zhong, H and Song, Y and Hu, S and Zhang, C and Li, L},
title = {Metagenomics-Metabolomics Reveals the Alleviation of Indole-3-Ethanol on Radiation-Induced Enteritis in Mice.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2502037},
doi = {10.4014/jmb.2502.02037},
pmid = {40730483},
issn = {1738-8872},
mesh = {Animals ; *Indoles/pharmacology/metabolism ; *Enteritis/drug therapy/etiology/metabolism/microbiology/pathology ; Mice ; Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; *Metabolomics/methods ; *Metagenomics/methods ; Male ; *Anti-Inflammatory Agents/pharmacology ; Colon/pathology/drug effects/radiation effects ; Cytokines/metabolism ; Interleukin-17/metabolism ; },
abstract = {Indole-3-ethanol (IEt), a small molecule metabolite from intestinal microbial tryptophan metabolism, has been established to have anti-inflammatory properties. However, its effect on radiation-induced enteritis has not been reported. Here, we aim to explore the effects and potential mechanisms of IEt on radiation enteritis. C57BL/6J mice were orally administered an IEt solution before radiation exposure. Inflammatory factors, including IL-17A, IFN-γ, IL-6 and IL-1β, were detected using enzyme-linked immunosorbent assay. Colonic histopathology was assessed through H&E staining. Subsequently, gut microbiota and its metabolites were analyzed using metagenomics and metabolomics. The results suggested that IEt alleviated radiation-induced enteritis, as evidenced by improved colonic structural integrity, decreased levels of pro-inflammatory factors like IL-17A, and the restoration of intestinal microecological and metabolic balance. IEt enriched the abundance of Lachnospiraceae family members, particularly the genus Roseburia - a known anti-inflammatory commensal. In addition, IEt upregulated the levels of metabolites with anti-inflammatory effects such as indole-3-carbinol, pteridine, and pyropheophorbide-a. Furthermore, Roseburia was significantly positively correlated with indole-3-carbinol and negatively correlated with the pro-inflammatory factor IL-17A. Therefore, IEt may alleviate radiation enteritis through Roseburia-indole-3-carbinol and Roseburia-IL-17A axes. This study revealed the potential mechanisms by which IEt alleviated radiation enteritis, providing a potential protective candidate for radiation enteritis.},
}

Animals
*Indoles/pharmacology/metabolism
*Enteritis/drug therapy/etiology/metabolism/microbiology/pathology
Mice
Gastrointestinal Microbiome/drug effects
Mice, Inbred C57BL
*Metabolomics/methods
*Metagenomics/methods
Male
*Anti-Inflammatory Agents/pharmacology
Colon/pathology/drug effects/radiation effects
Cytokines/metabolism
Interleukin-17/metabolism

@article {pmid40728669,
year = {2025},
author = {Priyadarsini, M and Dhoble, AS},
title = {Combination of flow cytometry and metagenomics to monitor the effect of raw vs digested manure on microbial diversity in anaerobic digestion of Napier grass.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {8},
pages = {963},
pmid = {40728669},
issn = {1573-2959},
support = {SPARC/2019-2020/P1570/SL//Scheme for Promotion of Academic and Research Collaboration (SPARC)/ ; },
mesh = {*Manure/microbiology ; Flow Cytometry ; Metagenomics ; *Poaceae/microbiology ; Anaerobiosis ; *Microbiota ; Biofuels ; Bacteria ; Archaea ; Animals ; },
abstract = {Microbiomes play a crucial role in anaerobic digestion (AD), by degrading the complex lignocellulosic biomass leading to biomethane production. This study emphasizes the role of microbial diversity and its impact on the digester's performance with raw (CD) and digested manure (ADS) as a source of microbiome and Napier grass (NG) as feedstock. The integration of flow cytometry and metagenomics provides a novel perspective on microbial dynamics during anaerobic digestion. Initially, the inocula (ADS and CD) had 354 bacterial and 8 archaeal genera in common that decreased to 39 bacteria and 1 archaeon at the end of experiment, indicating significant shift in microbial diversity during the process. Metagenome sequencing showed that Clostridium was the most abundant genera in NG digested with ADS, while Prevotella was in NG digested with CD. An approximately 2.45% increase in Clostridium in NG digested with ADS led to VFA accumulation and pH drop, inhibiting methanogens and lower biogas production. Most of the flow cytometric populations showed positive correlation with Prevotella suggesting its key role in breaking down of complex substrate. The population 2, 3, and 5 positively correlated to biogas production. NG digested with CD produced nearly twice biogas yield (1064.33 ± 119.97 mL) compared to ADS (508 ± 20.95 mL) which corresponds to the enhanced microbial activity in CD. These findings suggest that microbiome of CD might be better acclimatized for NG degradation than ADS as NG is often used as cattle fodder.},
}

*Manure/microbiology
Flow Cytometry
Metagenomics
*Poaceae/microbiology
Anaerobiosis
*Microbiota
Biofuels
Bacteria
Archaea
Animals

@article {pmid40728577,
year = {2025},
author = {Raziq, MF and Manzoor, H and Kayani, MUR},
title = {Non-small Cell Lung Cancer, Immunotherapy and the Influence of Gut Microbiome.},
journal = {Current microbiology},
volume = {82},
number = {9},
pages = {419},
pmid = {40728577},
issn = {1432-0991},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Carcinoma, Non-Small-Cell Lung/therapy/microbiology/immunology ; *Immunotherapy/methods ; *Lung Neoplasms/therapy/microbiology/immunology ; Immune Checkpoint Inhibitors/therapeutic use ; Animals ; },
abstract = {Lung cancer remains the second most commonly diagnosed cancer and the leading cause of cancer-related deaths worldwide. Non-small cell lung cancer (NSCLC), accounting for approximately 85% of lung cancer cases, is the most prevalent form. Treatment options for NSCLC include surgery, radiation therapy, chemotherapy, immunotherapy, and targeted drug therapies. Among these, immune checkpoint inhibitors targeting PD-1/PD-L1 have demonstrated significant potential, particularly in improving treatment outcomes. However, their clinical efficacy is impeded by challenges such as toxicity, resistance development, and variable patient responses. Emerging evidence highlights the critical role of the gut microbiome as an important modulator of immune responses in NSCLC, particularly in the context of anti-PD-1/PD-L1 therapies. Specific gut microbes, such as Akkermansia muciniphila, have been associated with improved responses to immunotherapy, suggesting that modulation of the gut microbiome may enhance treatment outcomes. This review discusses the current understanding of the influence of gut microbiome on NSCLC and its potential to improve the clinical efficacy of anti-PD-1/PD-L1 therapies. By integrating microbiome-based insights into personalized treatment strategies, we can overcome the limitations of current immunotherapy approaches and optimize patient outcomes. This review aims to serve as a resource for the scientific community by providing insights into how modulation of gut microbiome may enhance treatment outcomes in NSCLC patients receiving anti-PD-1/PD-L1 immunotherapy.},
}

Humans
*Gastrointestinal Microbiome
*Carcinoma, Non-Small-Cell Lung/therapy/microbiology/immunology
*Immunotherapy/methods
*Lung Neoplasms/therapy/microbiology/immunology
Immune Checkpoint Inhibitors/therapeutic use
Animals

@article {pmid40658106,
year = {2025},
author = {Chen, G and Wang, Y and Zhang, X and Jiang, K and Yu, M and Fang, L and Li, F},
title = {Periphyton-Driven Arsenic Methylation in Paddy Soils: The Crucial Role of Trophic Interactions.},
journal = {Environmental science & technology},
volume = {59},
number = {29},
pages = {15203-15214},
doi = {10.1021/acs.est.5c06047},
pmid = {40658106},
issn = {1520-5851},
mesh = {*Arsenic ; *Soil/chemistry ; Methylation ; Soil Microbiology ; Microbiota ; Oryza ; },
abstract = {Arsenic (As) methylation facilitated by periphyton in paddy soils is crucial for its biogeochemical cycling and thus its bioavailability. However, the key functional taxa and underlying interactive metabolisms remain unclear due to the high complexity of the periphytic microbiome. Here, we employ DNA-stable isotope probing with metagenomic binning analysis to uncover the critical role of intrinsic trophic interactions in stimulating As methylation within the periphyton in association with soil inorganic carbon. Abundance of As-methylating microorganisms in the periphyton increases by 2.1-fold after bicarbonate addition. Members of phototrophs are predominantly responsible for regulating the stability of the periphytic microbiome, of which photoautotrophs (e.g., Oscillatoriales) initiate carbon fixation and constitute a major portion of As-methylating populations. These phototrophs further offer requisite organic substrates such as polysaccharides for heterotrophic bacteria (e.g., Chitinophagales) that in return foster the growth of the periphytic community, while these taxa simultaneously detoxify As through biomethylation to secure their ecological niches in periphyton. Such a symbiotic metabolism between phototrophs and heterotrophs facilitates carbon sequestration and shapes the functional community, collaboratively determining methylated As production in paddy soils. These findings offer new insights into the influence of trophic interactions within the periphyton on As speciation with potential implications for element cycling and soil remediation in paddy soils.},
}

*Arsenic
*Soil/chemistry
Methylation
Soil Microbiology
Microbiota
Oryza

@article {pmid40586543,
year = {2025},
author = {Begmatov, S and Beletsky, AV and Mardanov, AV and Lukina, AP and Glukhova, LB and Karnachuk, OV and Ravin, NV},
title = {Novel lineages of bacteria with reduced genomes from the gut of farm animals.},
journal = {mSphere},
volume = {10},
number = {7},
pages = {e0029425},
pmid = {40586543},
issn = {2379-5042},
support = {//Ministry of Science and Higher Education of the Russian Federation (Minobrnauki of Russia)/ ; },
mesh = {Animals ; *Genome, Bacterial ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/classification/isolation & purification ; Feces/microbiology ; Phylogeny ; *Animals, Domestic/microbiology ; Metagenomics ; Cattle ; Sheep ; Horses/microbiology ; },
abstract = {Genome reduction and associated metabolic deficiencies have been described in various lineages of parasitic and symbiotic microorganisms that obtain essential nutrients from their partners, and in some free-living microorganisms that inhabit stable environments. The animal gut is a relatively stable ecosystem, characterized by an abundance of organic substances and a high concentration of microorganisms, which provides favorable conditions for the survival of microorganisms with reduced genomes. Metagenomic analysis of 49 samples of feces of farm animals (cows, sheep, yaks, and horses) revealed uncultured lineages of bacteria with reduced genomes (<1 Mbp): family UBA1242 (Christensenellales, Firmicutes), order Rs-D84 (Alphaproteobacteria), and family UBA9783 (Opitutales, Verrucomicrobiota), defined in genome-taxonomy database. Analysis of the genomes showed that these bacteria lacked pathways for the biosynthesis of amino acids, nucleotides, lipids, and many other essential metabolites. The UBA9783 genomes encoded a near-complete Embden-Meyerhof glycolytic pathway and the non-oxidative phase of the pentose phosphate pathway, while in UBA1242 and Rs-D84, these pathways are incomplete. All bacteria are limited to fermentative metabolism and lack aerobic and anaerobic respiratory pathways. All UBA9783 and some Rs-D84 genomes encoded F0F1-type ATP synthase and pyrophosphate-energized proton pump; they also can import and utilize peptides and some amino acids. While UBA9783 bacteria could thrive as specialized free-living organisms in the organic-rich gut environment, the UBA1242 and Rs-D84 lineages appear to have adopted the lifestyle of an obligate symbiont/parasite, obtaining metabolites from other cells.IMPORTANCEThe microbiota of the animal gastrointestinal tracts is a complex community of microorganisms which interact in a synergistic or antagonistic relationship and play key nutritional and metabolic roles. However, despite its importance, the gut microbiota of farm animals, especially its uncultured majority, remains largely unexplored. We performed a metagenomic analysis of the gut microbiome of farm animals and characterized three uncultured lineages of bacteria with reduced genomes (<1 Mbp) from the phyla Firmicutes, Proteobacteria, and Verrucomicrobiota. These bacteria were predicted to possess key metabolic deficiencies such as the inability to synthesize essential cell metabolites, suggesting their adaptation to the lifestyle of a symbiont/parasite, or a scavenger obtaining nutrients from the organic-rich gut environment. This study shows that genome reduction with metabolic specialization and adaptation to a partner-dependent lifestyle occurred through convergent evolution in several phylogenetically distant lineages of gut microbiota.},
}

Animals
*Genome, Bacterial
*Gastrointestinal Microbiome/genetics
*Bacteria/genetics/classification/isolation & purification
Feces/microbiology
Phylogeny
*Animals, Domestic/microbiology
Metagenomics
Cattle
Sheep
Horses/microbiology

@article {pmid40586542,
year = {2025},
author = {Bruno, JS and Heidrich, V and Restini, FCF and Alves, TMMT and Miranda-Silva, W and Knebel, FH and Cóser, EM and Inoue, LT and Asprino, PF and Camargo, AA and Fregnani, ER},
title = {Dental biofilm serves as an ecological reservoir of acidogenic pathobionts in head and neck cancer patients with radiotherapy-related caries.},
journal = {mSphere},
volume = {10},
number = {7},
pages = {e0025725},
pmid = {40586542},
issn = {2379-5042},
mesh = {Humans ; *Dental Caries/microbiology/etiology ; *Biofilms/growth & development ; *Head and Neck Neoplasms/radiotherapy/complications ; Male ; Female ; *Microbiota ; Middle Aged ; Aged ; *Bacteria/classification/genetics/isolation & purification ; Adult ; *Radiotherapy/adverse effects ; },
abstract = {UNLABELLED: Radiotherapy-related caries (RRC) is an aggressive and debilitating oral toxicity that affects half of the patients who undergo radiotherapy for head and neck cancer. However, the etiology of RRC is not fully established, and there are no clinically validated methods for preventing it. To gain a better understanding of the risk factors and the microbiome's role in causing RRC, we compared clinicopathological characteristics, oncological treatment regimens, oral health condition, and the oral microbiota at three different oral sites of radiotherapy-treated patients with (RRC+) and without radiotherapy-related caries (RRC-). We observed no significant differences between these groups in the clinicopathological characteristics and treatment regimens. However, RRC+ patients were older and had poorer oral health conditions at the start of the radiotherapy treatment, with a lower number of teeth and a higher proportion of rehabilitated teeth. RRC+ patients had lower microbiota diversity and the dental biofilm of RRC+ patients displayed striking alterations in microbiome composition compared to RRC- patients, including enrichment of acidogenic species and altered metabolic potential, with a higher abundance of genes linked to energy-related pathways associated with the synthesis of amino acids and sugars. We also compared the microbiota of RRC+ tissue with conventional caries tissue, revealing lower bacterial diversity and enrichment of Lactobacillaceae members in RRC+. The insights into the irradiated oral microbiota enhance the understanding of RRC etiology and highlight the potential for microbial-targeted therapies in its prevention and treatment.

IMPORTANCE: This study focuses on a dedicated collection of diverse oral sites to comprehensively investigate microbial differences between patients who develop RRC and those who do not. RRC is a severe oral disease that profoundly impacts on the oral health and overall quality of life of cancer survivors. Leveraging shotgun metagenomics, we characterize the unique microbial variations in in vivo irradiated dental biofilms, unveiling novel insights into the microbial ecology of radiotherapy-treated patients. Furthermore, this research integrates extensive data on oral health and oncological profiles, providing a comprehensive understanding of the intricate relationship between oral microbial communities and the outcomes of radiotherapy-induced toxicity.},
}

Humans
*Dental Caries/microbiology/etiology
*Biofilms/growth & development
*Head and Neck Neoplasms/radiotherapy/complications
Male
Female
*Microbiota
Middle Aged
Aged
*Bacteria/classification/genetics/isolation & purification
Adult
*Radiotherapy/adverse effects

@article {pmid40543204,
year = {2025},
author = {Yang, J and Kim, JS and Jeon, HW and Lee, J and Seo, JH},
title = {Integrated culture-based and metagenomic profiling of airborne and surface-deposited bacterial communities in residential environments.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {382},
number = {},
pages = {126703},
doi = {10.1016/j.envpol.2025.126703},
pmid = {40543204},
issn = {1873-6424},
mesh = {*Air Microbiology ; *Air Pollution, Indoor/analysis/statistics & numerical data ; *Bacteria/genetics/classification/isolation & purification ; *Environmental Monitoring ; Housing ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Microbiota ; Humans ; },
abstract = {Indoor environments host diverse microbial communities, where airborne and surface-deposited bacteria contribute to human exposure and potential health risks. This study applies metagenomic analysis to examine bacterial diversity in residential apartments, focusing on four key indoor spaces: kitchens, living rooms, toilets, and bedrooms. Airborne bacteria were collected using a culture-based air sampler and surface-deposited bacteria were collected via swabbing of high-contact areas; both were analyzed through 16S rRNA gene sequencing and bioinformatics processing. Airborne bacterial communities were primarily composed of Staphylococcus, Bacillus, and Enhydrobacter, whereas surface-deposited bacteria varied by location, with Streptococcus and Staphylococcus being most common on high-contact surfaces. Overall, surface-deposited bacterial diversity was greater than that of airborne communities, highlighting their distinct but interconnected roles in indoor microbial ecosystems. Functional pathway analysis suggested that indoor bacterial communities may harbor metabolic functions, as well as antibiotic resistance and virulence-related pathways, pointing to potential health concerns. Principal component analysis (PCA) showed clear distinctions between airborne and surface-deposited bacterial communities. These findings highlight the need for space-specific microbial management strategies, such as improved ventilation and surface hygiene, to reduce exposure risks and promote healthier indoor environments.},
}

*Air Microbiology
*Air Pollution, Indoor/analysis/statistics & numerical data
*Bacteria/genetics/classification/isolation & purification
*Environmental Monitoring
Housing
Metagenomics
RNA, Ribosomal, 16S/genetics
Microbiota
Humans

@article {pmid40532815,
year = {2025},
author = {Pan, D and Sun, H and Liu, Y and Wang, J and Kuang, Y and Shi, T and Zhang, H},
title = {Mobilome dominates fomesafen-responsive dissemination of antibiotic resistome in manure-amended agricultural soils.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {382},
number = {},
pages = {126686},
doi = {10.1016/j.envpol.2025.126686},
pmid = {40532815},
issn = {1873-6424},
mesh = {Manure ; *Soil Microbiology ; Agriculture ; *Herbicides ; Soil/chemistry ; *Soil Pollutants ; *Drug Resistance, Microbial/genetics ; *Benzamides ; Microbiota ; },
abstract = {Pesticides are increasingly perceived as emerging drivers in the spread of antibiotic resistance genes (ARGs) within agroecosystems. Pesticides with longer half-lives tend to impose persistent stresses on soil microbiomes, yet the selection for ARG dissemination remains overlooked. Focusing on a widely used long residual herbicide fomesafen, we examined recommended dose-based selection on the dissemination of ARGs in agricultural soils with or without manure amendment. The degradation half-lives of fomesafen in the blank soils and manure-amended soils were 35.77-124.00 and 20.00-73.27 d, respectively. After 42-d exposure, the total abundances of ARGs in the fomesafen-treated manure-amended soils at exposure concentrations of 1 and 5 mg/kg were 1.20- and 1.36-fold higher than that in the controls, with the changes of mobile genetic elements (MGEs) reaching 1.24-2.22 folds; while no significant change was observed in the blank soils. Furthermore, no significant change was observed in either bacterial communities or ARG-carrying metagenome-assembled genomes in both manure-amended soils and blank soils under fomesafen selection. Variation partition analysis suggested that 24.42%-25.41% of the variations in ARGs could be individually explained by MGEs, while only 13.47%-13.75% by bacterial communities. Overall, these findings demonstrate that MGE-mediated horizontal transfer predominates fomesafen-responsive dissemination of ARGs in manure-amended agriculture soils and underscores the urgency of re-evaluating agricultural practices involving co-application of manures and long residual herbicides.},
}

Manure
*Soil Microbiology
Agriculture
*Herbicides
Soil/chemistry
*Soil Pollutants
*Drug Resistance, Microbial/genetics
*Benzamides
Microbiota

@article {pmid40516682,
year = {2025},
author = {Sadah Al Azzawi, DH and Jalali, A and Rezaei, M},
title = {Metagenomic insights into bacterial communities and antibiotic resistance genes in landfill-impacted waters.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {382},
number = {},
pages = {126663},
doi = {10.1016/j.envpol.2025.126663},
pmid = {40516682},
issn = {1873-6424},
mesh = {*Waste Disposal Facilities ; *Bacteria/genetics/classification ; *Drug Resistance, Microbial/genetics ; *Water Pollutants, Chemical/analysis ; Metals, Heavy/analysis ; Metagenomics ; Iran ; Environmental Monitoring ; Genes, Bacterial ; *Water Microbiology ; Microbiota ; },
abstract = {Municipal landfills are significant sources of environmental and microbial pollution, impacting groundwater and surface water quality. This study investigated the microbial community composition and antibiotic resistance genes (ARGs) in water downstream of landfills of Gilan, Mazandaran, and Golestan provinces, Iran. Water samples were collected from seven sites, and shotgun metagenomic sequencing was used to analyze microbial diversity and ARGs. Heavy metals and BTEX (benzene, toluene, ethylbenzene, and xylene) compounds were measured using inductively coupled plasma (ICP), and gas chromatography-mass spectrometry (GC-MS) methods, respectively. Pseudomonadaceae and Enterobacteriaceae were the most abundant bacterial families, with efflux pump ARGs being the most prevalent. Concentrations of arsenic and cadmium exceeded WHO and US-EPA standards at all sites. Significant positive correlations were observed between Pseudomonadaceae abundance and lead concentration (r = 0.998, p = 0.031, CI [0.966, 0.999]), and between Enterobacteriaceae abundance and chromium concentration (r = 0.999, p = 0.0078, CI [0.993, 1.000]). A significant negative correlation was found between the abundance of the two-component system (TCS) gene class and BTEX concentration (r = -0.457, p = 0.014, CI [-0.72, -0.09]). Additionally, aluminum concentration negatively correlated with antibiotic inactivation (r = 0.999, p = 0.018, CI [-1.000, -0.997]) and antibiotic target protection classes (r = -0.997, p = 0.048, CI [-0.999, -0.990]). These findings indicate that landfill sites significantly influence bacterial communities, promoting resistance to heavy metals and pollutants. The abundance of ARGs near landfills suggests microbial adaptation to pollution, highlighting the need for improved waste management to mitigate the spread of antibiotic resistance.},
}

*Waste Disposal Facilities
*Bacteria/genetics/classification
*Drug Resistance, Microbial/genetics
*Water Pollutants, Chemical/analysis
Metals, Heavy/analysis
Metagenomics
Iran
Environmental Monitoring
Genes, Bacterial
*Water Microbiology
Microbiota

@article {pmid40111891,
year = {2025},
author = {Díez-Madueño, K and Montero, I and Fernández-Gosende, M and Martínez-Álvarez, N and Hidalgo-Cantabrana, C and de la Cueva Dobao, P and Coto-Segura, P},
title = {Compositional and Functional Profile of Gut Microbiota in a Cohort of Adult Spanish Patients with Atopic Dermatitis Using Metagenomics: A Cross-Sectional Study.},
journal = {Dermatitis : contact, atopic, occupational, drug},
volume = {36},
number = {4},
pages = {358-364},
doi = {10.1089/derm.2024.0536},
pmid = {40111891},
issn = {2162-5220},
mesh = {Humans ; *Dermatitis, Atopic/microbiology ; Cross-Sectional Studies ; *Gastrointestinal Microbiome/genetics ; Adult ; Female ; Male ; Metagenomics ; *Dysbiosis/microbiology ; Feces/microbiology ; Middle Aged ; Spain ; Case-Control Studies ; Young Adult ; },
abstract = {Background: The role of gut dysbiosis in the pathophysiology of atopic dermatitis (AD) through immune system (IS) imbalance is a novel line of investigation currently under discussion. This study aimed to characterize compare the composition and functional profile of the gut microbiota (GM) between adults with AD and healthy individuals. Methods: Observational cross-sectional study, where fecal samples from 70 adults (38 patients and 32 controls) were analyzed using metagenomics and bioinformatics. Results: Differences between the GM of patients with AD and healthy individuals were demonstrated. Reduced microbial diversity was found in subjects with AD. Bacterial species with lower abundance primarily belonged to the families Ruminococcaceae, Akkermansiaceae, and Methanobacteriaceae. Several microbial metabolic pathways were found to be decreased in patients with AD, including amino acid biosynthesis, vitamin biosynthesis, fatty acids and lipids biosynthesis, and energy metabolism. Conclusion: Adults with AD exhibited a distinct GM compared to healthy individuals. Changes were demonstrated both compositionally and functionally. Further investigation is mandatory to elucidate the potential link and causal relationship between gut dysbiosis and AD, which may be crucial for a deeper understanding of the disease's pathophysiology and the development of novel therapeutic approaches.},
}

Humans
*Dermatitis, Atopic/microbiology
Cross-Sectional Studies
*Gastrointestinal Microbiome/genetics
Adult
Female
Male
Metagenomics
*Dysbiosis/microbiology
Feces/microbiology
Middle Aged
Spain
Case-Control Studies
Young Adult

@article {pmid40724992,
year = {2025},
author = {Rušanac, A and Škibola, Z and Matijašić, M and Čipčić Paljetak, H and Perić, M},
title = {Microbiome-Based Products: Therapeutic Potential for Inflammatory Skin Diseases.},
journal = {International journal of molecular sciences},
volume = {26},
number = {14},
pages = {},
doi = {10.3390/ijms26146745},
pmid = {40724992},
issn = {1422-0067},
support = {NPOO.C3.2.R3-I1.04.0240//European Regional Development Fund/ ; KK.01.2.1.02.0137//European Regional Development Fund/ ; IP.1.1.03.0157//European Regional Development Fund/ ; },
mesh = {Humans ; *Microbiota/drug effects ; Probiotics/therapeutic use ; Prebiotics/administration & dosage ; *Skin Diseases/microbiology/therapy ; Dysbiosis/microbiology/therapy ; Skin/microbiology ; Animals ; Psoriasis/microbiology/therapy ; Dermatitis, Atopic/microbiology/therapy ; },
abstract = {Maintaining a balanced skin microbiota is essential for skin health, whereas disruptions in skin microbiota composition, known as dysbiosis, can contribute to the onset and progression of various skin disorders. Microbiota dysbiosis has been associated with several inflammatory skin conditions, including atopic dermatitis, seborrheic dermatitis, acne, psoriasis, and rosacea. Recent advances in high-throughput sequencing and metagenomic analyses have provided a deeper understanding of the skin microbial communities in both health and disease. These discoveries are now being translated into novel therapeutic approaches aimed at restoring microbial balance and promoting skin health through microbiome-based interventions. Unlike conventional therapies that often disrupt the microbiota and lead to side effects or resistance, microbiome-based products offer a more targeted strategy for preventing and managing inflammatory skin diseases. These products, which include probiotics, prebiotics, postbiotics, and live biotherapeutic agents, are designed to modulate the skin ecosystem by enhancing beneficial microbial populations, suppressing pathogenic strains, and enhancing immune tolerance. As a result, they represent a promising class of products with the potential to prevent, manage, and even reverse inflammatory skin conditions. However, realizing the full therapeutic potential of microbiome-based strategies in dermatology will require continued research, robust clinical validation, and clear regulatory frameworks.},
}

Humans
*Microbiota/drug effects
Probiotics/therapeutic use
Prebiotics/administration & dosage
*Skin Diseases/microbiology/therapy
Dysbiosis/microbiology/therapy
Skin/microbiology
Animals
Psoriasis/microbiology/therapy
Dermatitis, Atopic/microbiology/therapy

@article {pmid40723458,
year = {2025},
author = {Penalba-Iglesias, D and Robas-Mora, M and González-Reguero, D and Fernández-Pastrana, VM and Probanza, A and Jiménez-Gómez, PA},
title = {Use of Bacillus pretiosus and Pseudomonas agronomica for the Synthesis of a Valorized Water Waste Treatment Plant Waste as a Biofertilizer Intended for Quercus pyrenaica L. Fertigation.},
journal = {Biology},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/biology14070902},
pmid = {40723458},
issn = {2079-7737},
support = {TED2021-132285A-I00//Next Generation Funds/ ; },
abstract = {The loss of hectares of forest areas has become a global issue that has worsened over recent years due to unsustainable human activities. In a context of limited availability of productive land, it is urgent to adopt efficient strategies to recover the affected natural areas. Actions based on a circular economy, such as the use of organic chemical matrices recovered from water waste treatment plant waste, have proven to be effective. In this regard, the addition of plant growth-promoting bacteria (PGPB), such as Bacillus pretiosus and Pseudomonas agronomica, can contribute to the chemical treatment, favoring the recovery of soils, accelerating the recovery of vegetation cover, and inducing an increase in biodiversity. In this research, the effect of bio-fertigation under controlled laboratory conditions in Quercus pyrenaica is evaluated. After a thirty-six-week trial, the biometric and nutritional parameters of the plants were harvested and measured, and the diversity and composition of the metagenomes of their rhizospheres were evaluated. As well, the cenoantibiogram and the metabolic diversity were measured. The results showed that the use of these biofertilizers increased the variables related to plant production, quality of plant composition as an indirect means of their resilience, as well as an increase in rhizospheric microbial diversity and a reduction in their MIC resistance to the most widely used antibiotics. For all these reasons, the use of the biofertilizer result of the combination of WWTP waste, Bacillus pretiosus, and Pseudomonas agronomica is postulated as an environmentally friendly strategy that can contribute to the recovery of potential oak forest areas.},
}

@article {pmid40721426,
year = {2025},
author = {Yang, Y and Ye, M and Song, Y and Xing, W and Zhao, X and Li, Y and Shen, J and Zhou, J and Arikawa, K and Wu, S and Song, Y and Xu, N},
title = {Gut microbiota and SCFAs improve the treatment efficacy of chemotherapy and immunotherapy in NSCLC.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {146},
doi = {10.1038/s41522-025-00785-9},
pmid = {40721426},
issn = {2055-5008},
support = {2020YFC2003700//National Key R&D Plan/ ; ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; 20Z11901000, 20DZ2261200, 20XD1401200, 22Y11900800//Science and Technology Commission of Shanghai Municipality/ ; SHDC2020CR5010-002//Clinical Research Plan of SHDC/ ; shslczdzk02201//Shanghai Municipal Key Clinical Specialty/ ; ZY(2021-2023)-0207-01//Shanghai Municipal Health Commission and Shanghai Municipal Administrator of Traditional Chinese Medicine/ ; 81401877, 82130001, and 82272243//National Natural Science Foundation of China/ ; 81401877, 82130001, and 82272243//National Natural Science Foundation of China/ ; },
mesh = {*Gastrointestinal Microbiome ; Humans ; *Carcinoma, Non-Small-Cell Lung/therapy/microbiology/drug therapy ; *Immunotherapy/methods ; Animals ; *Lung Neoplasms/therapy/microbiology/drug therapy ; Mice ; *Fatty Acids, Volatile/metabolism ; Fecal Microbiota Transplantation ; RNA, Ribosomal, 16S/genetics ; Treatment Outcome ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Female ; Male ; Metagenomics ; Middle Aged ; Aged ; Dysbiosis/microbiology ; Antineoplastic Agents/therapeutic use ; },
abstract = {The role of gut dysbiosis in shaping immunotherapy responses is well-recognized, yet its effect on the therapeutic efficacy of chemotherapy and immunotherapy combinations remains poorly understood. We analyzed gut microbiota in non-small cell lung cancer (NSCLC) patients treated with chemo-immunotherapy, comparing responders and non-responders using 16S rRNA sequencing. Responders showed higher microbial richness and abundance of specific genera like Faecalibacterium and Subdoligranulum, and the phylum Firmicutes. Support vector machine (SVM), a machine learning model based on microbial composition, predicted treatment efficacy with the area under the curve (AUC) values of 0.763 for genera and 0.855 for species. Metagenomic analysis revealed significant differences in metabolic pathways, with responders exhibiting higher short-chain fatty acids (SCFAs) production. Fecal microbiota transplantation (FMT) and SCFAs supplementation in mouse models enhanced treatment efficacy by promoting effector T cell activity in tumors. Our study suggests that gut microbiota, through SCFAs production, regulates chemo-immunotherapy efficacy, offering new strategies to improve NSCLC treatment outcomes.},
}

*Gastrointestinal Microbiome
Humans
*Carcinoma, Non-Small-Cell Lung/therapy/microbiology/drug therapy
*Immunotherapy/methods
Animals
*Lung Neoplasms/therapy/microbiology/drug therapy
Mice
*Fatty Acids, Volatile/metabolism
Fecal Microbiota Transplantation
RNA, Ribosomal, 16S/genetics
Treatment Outcome
*Bacteria/classification/genetics/isolation & purification/metabolism
Female
Male
Metagenomics
Middle Aged
Aged
Dysbiosis/microbiology
Antineoplastic Agents/therapeutic use

@article {pmid40720840,
year = {2025},
author = {Slizovskiy, IB and Gaire, TN and Ferm, PM and Odland, CA and Dee, SA and Nerem, J and Bravo, JE and Kimball, AD and Boucher, C and Noyes, NR},
title = {Reducing skin microbiome exposure impacts through swine farm biosecurity.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
doi = {10.1093/gigascience/giaf062},
pmid = {40720840},
issn = {2047-217X},
support = {/NH/NIH HHS/United States ; 1R01AI141810-01//National Institute of Allergy and Infectious Diseases/ ; 5U54OH010170-13A/OH/NIOSH CDC HHS/United States ; },
mesh = {*Microbiota ; *Skin/microbiology ; Animals ; Swine/microbiology ; Humans ; Farms ; *Biosecurity ; *Occupational Exposure ; Female ; Male ; Adult ; Bacteria/genetics/classification/isolation & purification ; Longitudinal Studies ; Animal Husbandry ; Skin Microbiome ; },
abstract = {BACKGROUND: Livestock work is unique due to worker exposure to animal-associated microbiomes within the workplace. Swine workers are a unique cohort within the US livestock labor force, as they have direct daily contact with pigs and undertake mandatory biosecurity interventions. However, investigating this occupational cohort is challenging, particularly within tightly regulated commercial swine operations. Thus, little is known about the impacts of animal exposure and biosecurity protocols on the swine worker microbiome. We obtained unique samples from US swine workers, using a longitudinal study design to investigate temporal microbiome dynamics.

RESULTS: We observed a significant increase in bacterial DNA load on worker skin during the workday, with concurrent changes in the composition and abundance of microbial taxa, resistance genes, and mobile genetic elements. However, mandatory showering at the end of the workday partially returned the skin's microbiome and resistome to their original state.

CONCLUSIONS: These novel results from a human cohort demonstrate that existing biosecurity practices can ameliorate work-associated microbiome impacts.},
}

*Microbiota
*Skin/microbiology
Animals
Swine/microbiology
Humans
Farms
*Biosecurity
*Occupational Exposure
Female
Male
Adult
Bacteria/genetics/classification/isolation & purification
Longitudinal Studies
Animal Husbandry
Skin Microbiome

@article {pmid40719990,
year = {2025},
author = {Naqvi, SAH and Umar, UUD and Rehman, AU},
title = {Beneficial communities from core bacterial microbiota of Oryza sativa L. soil and leaves perform dynamic role in growth promotion and suppression of bacterial leaf blight.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {8},
pages = {285},
pmid = {40719990},
issn = {1573-0972},
mesh = {*Oryza/microbiology/growth & development ; *Soil Microbiology ; *Plant Leaves/microbiology/growth & development ; Xanthomonas/pathogenicity/growth & development ; *Bacteria/classification/genetics/isolation & purification ; *Plant Diseases/microbiology/prevention & control ; *Microbiota/genetics ; Rhizosphere ; RNA, Ribosomal, 16S/genetics ; Pakistan ; Biological Control Agents ; Soil/chemistry ; Metagenomics ; Phylogeny ; },
abstract = {Bacterial leaf blight (BLB), caused by Xanthomonas oryzae pv. oryzae (Xoo), severely threatens global rice production, highlighting the urgent need for sustainable alternatives to chemical pesticides. This study investigates the rhizosphere and phyllosphere microbiomes of Oryza sativa in Punjab, Pakistan, to identify native biocontrol agents (BCAs) with potential to suppress BLB. Using 16S rRNA amplicon sequencing (V3-V9 regions), we analyzed soil and leaf samples from 10 agricultural districts. Microbial diversity, community structure, and functional potential were assessed via bioinformatics tools (QIIME 2, DADA2, PICRUSt2), with a focus on taxa antagonistic to Xoo. Healthy rhizospheres exhibited significantly higher alpha diversity (Shannon index: 6.8 vs. 4.2 in leaves; *p* < 0.001), dominated by copiotrophic taxa (Proteobacteria, Bacteroidetes) linked to organic inputs and root exudates. Diseased soils favored oligotrophic Actinobacteria and Chloroflexi. Functional metagenomics revealed enrichment of siderophore biosynthesis, antibiotic production, and nutrient-cycling genes in healthy soils. Antagonistic genera (Bacillus, Pseudomonas, Streptomyces) demonstrated chitinase and surfactin activity against Xoo, while diseased samples showed elevated Xanthomonas and Erwinia abundances correlating with BLB severity. Native BCAs outperformed non-native strains in colonization and nutrient competition, highlighting their adaptability to local agroecological conditions. Our findings position native BCAs as pivotal tools for BLB suppression and sustainable agriculture, reducing reliance on synthetic chemicals. Field trials confirmed that microbial consortia formulations reduced BLB incidence by 40% and increased yield by 18%. These findings highlight the potential of microbiome-driven strategies to mitigate BLB, reduce chemical reliance, and foster sustainable agricultural practices. Future work should integrate multi-omics approaches to optimize microbial solutions for climate resilience and scale their adoption through policy frameworks.},
}

*Oryza/microbiology/growth & development
*Soil Microbiology
*Plant Leaves/microbiology/growth & development
Xanthomonas/pathogenicity/growth & development
*Bacteria/classification/genetics/isolation & purification
*Plant Diseases/microbiology/prevention & control
*Microbiota/genetics
Rhizosphere
RNA, Ribosomal, 16S/genetics
Pakistan
Biological Control Agents
Soil/chemistry
Metagenomics
Phylogeny

@article {pmid40719366,
year = {2025},
author = {Wang, X and Wang, N and Gao, T and Zhang, Y and Fu, Z and Zhao, Y and Huang, Y and Zheng, X and Gao, X and Lu, L and Yang, L},
title = {Symptom-specific gut microbial and metabolic profiles in ADHD reveal SCFA deficiency as a Key pathogenic mechanism.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2537755},
doi = {10.1080/19490976.2025.2537755},
pmid = {40719366},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/physiology ; *Attention Deficit Disorder with Hyperactivity/microbiology/metabolism ; Animals ; Humans ; Mice ; Male ; Female ; *Fatty Acids, Volatile/metabolism ; Feces/microbiology/chemistry ; Fecal Microbiota Transplantation ; Child ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Metabolome ; Adolescent ; Metabolomics ; },
abstract = {Previous evidence links gut microbiota to attention-deficit/hyperactivity disorder (ADHD) through the gut-brain axis. However, the specific microbiota contributing to symptoms remain unclear. To characterize the gut microbial profile related to different symptoms and explore the mediation mechanism between microbiota alterations and the core ADHD symptoms, we conducted shotgun metagenomic sequencing and fecal metabolomics analysis on 94 ADHD patients and 94 age- and gender-matched controls. Microbial characteristics of three subgroups exhibiting different ADHD core symptom presentations were analyzed. We developed a metabolic model and conducted causal mediation analyses to examine how metabolites connect the microbiota to the symptoms. Fecal microbiota transplantation in mice was employed to validate the findings. The redundancy analysis identified ADHD symptoms as environmental gradients and explained the changes in beta diversity (F = 1.345, pFDR = 0.015). Greater gut microbial alterations were observed in combined presentations (ADHD-C). Several beneficial bacteria involved in short-chain fatty acid synthesis were found to be downregulated, with Lactobacillus sanfranciscensis notably linked to all three core symptoms (p.adj = 1.04E-13; p.adj = 5.07E-07; p.adj = 2.61E-05). Various taxa, functional pathways, and metabolites associated with specific ADHD symptom domains were identified. Imidazoleacetic acid partially mediated the effects between Lactobacillus sanfranciscensis and inattention (p = 0.012). In mice subjected to feces from ADHD patients with a low abundance of Lactobacillus sanfranciscensis, treatment with this strain greatly improved both hyperactivity (t = 2.665, p = 0.0237) and inattention (t = 2.389, p = 0.0380), while acetate supplementation only alleviated inattention (t = 2.362, p = 0.0398). Our findings suggest that different ADHD symptoms were related to common and different gut microbiota and metabolites. Fecal microbiota transplantation in mice validated the hypothesis that gut microbial composition affects ADHD symptoms through metabolic alterations. This study provides more insight into the mechanisms underlying metabolic disturbances in ADHD and elucidates the role of gut microbiota in these processes.},
}

*Gastrointestinal Microbiome/physiology
*Attention Deficit Disorder with Hyperactivity/microbiology/metabolism
Animals
Humans
Mice
Male
Female
*Fatty Acids, Volatile/metabolism
Feces/microbiology/chemistry
Fecal Microbiota Transplantation
Child
*Bacteria/classification/metabolism/genetics/isolation & purification
Metabolome
Adolescent
Metabolomics

@article {pmid40715283,
year = {2025},
author = {Tan, JH and Liew, KJ and Sani, RK and Samanta, D and Pointing, SB and Chan, KG and Goh, KM},
title = {Microbial diversity and metabolic predictions of high-temperature streamer biofilms using metagenome-assembled genomes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {27297},
pmid = {40715283},
issn = {2045-2322},
mesh = {*Biofilms/growth & development ; *Hot Springs/microbiology ; *Metagenome ; Hot Temperature ; *Bacteria/genetics/metabolism/classification ; Microbiota ; Phylogeny ; Biodiversity ; Genome, Bacterial ; Metagenomics/methods ; Malaysia ; },
abstract = {High-temperature streamer biofilm communities (SBCs) are often dominated by Aquificota, which can comprise over 90% of the microbial population in shallow water channels, such as those found at Mammoth hot springs of Yellowstone National Park and the Rehai hot springs in China. This study examines SBCs from the Dusun Tua (DT) hot spring in Malaysia (75 °C, pH 7.6), where Aquificota accounted for only ~ 35% of the total amplicon sequence variants. Amplicon and hybrid metagenomic sequencing revealed a more balanced microbial community, co-dominated by Aquificota, Chloroflexota, Desulfobacterota, Bacteroidota, Deinococcota, and Candidatus Hydrothermae, along with Thermoproteota and Micrarchaeota. To our knowledge, the co-dominance of Aquificota and Chloroflexota in SBCs has not been previously reported. The unexpected abundance of Chloroflexota may stem from dispersal from upstream Cyanobacteriota-Chloroflexota biofilms, contributing to community diversification. Genome-resolved analyses identified more than 60 medium- to high-quality metagenome-assembled genomes (MAGs), suggesting that biofilm formation was initially driven by chemoautotrophic sulfur oxidation and CO2 fixation, followed by the gradual integration of heterotrophic taxa. Nitrogen cycling and hydrogen oxidation are likely to contribute additional sources of energy. The presence of diverse CAZymes suggests that plant litter may serve as an additional carbon source. Genome-centric analyses across multiple phyla indicated that extracellular polymeric substances (EPS), curli fibers, and other matrix components contribute to the biofilm matrix, enhancing structural resilience and supporting persistence under harsh conditions. Overall, this study highlights the distinct microbial ecology of the DT SBC and broader metabolic roles beyond Aquificota dominance. The genes identified in this study may hold biotechnological potential and serve as a valuable resource for future enzyme discovery and functional screening.},
}

*Biofilms/growth & development
*Hot Springs/microbiology
*Metagenome
Hot Temperature
*Bacteria/genetics/metabolism/classification
Microbiota
Phylogeny
Biodiversity
Genome, Bacterial
Metagenomics/methods
Malaysia

@article {pmid40715043,
year = {2025},
author = {Duchesneau, K and Aldeguer-Riquelme, B and Petro, C and Makke, G and Green, M and Tfaily, M and Wilson, R and Roth, SW and Johnston, ER and Kluber, LA and Schadt, CW and Trejo, JB and Callister, SJ and Purvine, SO and Chanton, JP and Hanson, PJ and Tringe, S and Eloe-Fadrosh, E and Glavina Del Rio, T and Konstantinidis, KT and Kostka, JE},
title = {Northern peatland microbial communities exhibit resistance to warming and acquire electron acceptors from soil organic matter.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6869},
pmid = {40715043},
issn = {2041-1723},
support = {DE-SC0023297//U.S. Department of Energy (DOE)/ ; DE-SC0012088//U.S. Department of Energy (DOE)/ ; DE-AC05-76RL01830//U.S. Department of Energy (DOE)/ ; },
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Microbiota/genetics/physiology ; Methane/metabolism ; Metagenome ; Carbon/metabolism ; Climate Change ; Bacteria/metabolism/genetics/classification ; Global Warming ; Ecosystem ; Electrons ; },
abstract = {The response of microbial communities that regulate belowground carbon turnover to climate change drivers in peatlands is poorly understood. Here, we leverage a whole ecosystem warming experiment to elucidate the key processes of terminal carbon decomposition and community responses to temperature rise. Our dataset of 697 metagenome-assembled genomes (MAGs) represents the microbial community from the surface (10 cm) to 2 m deep into the peat column, with only 3.7% of genomes overlapping with other well-studied peatlands. Community composition has yet to show a significant response to warming after 3 years, suggesting that metabolically diverse soil microbial communities are resistant to climate change. Surprisingly, abundant and active methanogens in the genus Candidatus Methanoflorens, Methanobacterium, and Methanoregula show the potential for both acetoclastic and hydrogenotrophic methanogenesis. Nonetheless, the predominant pathways for anaerobic carbon decomposition include sulfate/sulfite reduction, denitrification, and acetogenesis, rather than methanogenesis based on gene abundances. Multi-omics data suggest that organic matter cleavage provides terminal electron acceptors, which together with methanogen metabolic flexibility, may explain peat microbiome composition resistance to warming.},
}

*Soil Microbiology
*Soil/chemistry
*Microbiota/genetics/physiology
Methane/metabolism
Metagenome
Carbon/metabolism
Climate Change
Bacteria/metabolism/genetics/classification
Global Warming
Ecosystem
Electrons

@article {pmid40714398,
year = {2025},
author = {Wu, L and Yan, M and Huang, X and Liao, H and Bao, D and Ge, Y and Wang, S and Xia, X},
title = {Temperature-mediated shift from competitive to facilitative interactions between lactic acid bacteria and bacillus species in daqu fermentation: Insights from metagenomics, dual RNA-seq, and coculture analysis.},
journal = {International journal of food microbiology},
volume = {442},
number = {},
pages = {111352},
doi = {10.1016/j.ijfoodmicro.2025.111352},
pmid = {40714398},
issn = {1879-3460},
abstract = {Daqu, a pivotal starter that defines the flavor profile and quality of Baijiu, undergoes dynamic temperature changes during its production, significantly influencing the microbial community structure and function. Although the importance of fermentation temperature in shaping microbial biodiversity is well-recognized, its impact on microbial interaction dynamics and the underlying mechanisms remains poorly understood. This study integrates metagenomics, dual RNA-seq, and coculture experiments to elucidate temperature-dependent microbial interactions during Daqu fermentation. Metagenomic analysis revealed that lactic acid bacteria (LAB) and Bacillus are dominant genera with distinct thermal preferences that nevertheless coexist throughout the fermentation process. Elevated temperature stress was found to enhance positive microbial interactions within the Daqu ecosystem. Dual RNA-seq analysis uncovered temperature-responsive gene expression patterns associated with oxidative stress, metabolic capacity, and environmental information processing in representative LAB and Bacillus strains. Guided by these multi-omics findings, co-culture assays demonstrated a temperature-dependent shift in microbial interaction modes. At 30 °C, Lactococcus lactis secretes lactic acid that inhibits the growth of Bacillus subtilis, whereas at 50 °C, B. subtilis alleviates oxidative stress in L. lactis by producing cobalamin, thereby enabling short-term rescue and sustained coexistence over serial transfers. These findings provide critical insights into the temperature-driven modulation of microbial interactions, enhancing the precision and manageability of the Daqu fermentation process.},
}

@article {pmid40700599,
year = {2025},
author = {Mofidifar, S and Tefagh, M},
title = {Reducing redundancy and enhancing accuracy through a phylogenetically-informed microbial community metabolic modeling approach.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {7},
pages = {},
pmid = {40700599},
issn = {1367-4811},
mesh = {*Phylogeny ; *Models, Biological ; *Microbiota ; *Metagenomics/methods ; *Computational Biology/methods ; Computer Simulation ; },
abstract = {MOTIVATION: Metabolic modeling has emerged as a powerful tool for predicting community functions. However, current modeling approaches face significant challenges in balancing the metabolic trade-offs between individual and community-level growth. In this study, we investigated the effect of metabolic relatedness among taxa on growth rate calculations by merging related taxa based on their metabolic similarity, introducing this approach as PhyloCOBRA.

RESULTS: This approach enhanced the accuracy and efficiency of microbial community simulations by combining genome-scale metabolic models (GEMs) of closely related organisms, aligning with the concepts of niche differentiation and nestedness theory. To validate our approach, we implemented PhyloCOBRA within the MICOM and OptCom package (creating PhyloMICOM and PhyloOptCom, respectively), and applied it to metagenomic data from 186 individuals and four-species synthetic community (SynCom). Our results demonstrated significant improvement in the accuracy and reliability of growth rate predictions compared to the standard methods. Sensitivity analysis revealed that PhyloMICOM models were more robust to random noise, while Jaccard index calculations showed a reduction in redundancy, highlighting the enhanced specificity of the generated community models. Furthermore, PhyloMICOM reduced the computational complexity, addressing a key concern in microbial community simulations. This approach marks a significant advancement in community-scale metabolic modeling, offering a more stable, efficient, and ecologically relevant tool for simulating and understanding the intricate dynamics of microbial ecosystems.

PhyloCOBRA implementations are available as extensions to the MICOM packages and can be accessed at https://github.com/sepideh-mofidifar/PhyloCOBRA.},
}

*Phylogeny
*Models, Biological
*Microbiota
*Metagenomics/methods
*Computational Biology/methods
Computer Simulation

@article {pmid40674041,
year = {2025},
author = {Bisson, G and Comuzzi, C and FitzGerald, JA and Mukherjee, A and Renoldi, N and Innocente, N and Beresford, T and Mathur, H and Cotter, PD and Marino, M},
title = {Development of a bio-functional fermented soy beverage supplemented with microbial exopolysaccharides and its effect on the human gut microbiome in vitro.},
journal = {Food & function},
volume = {16},
number = {15},
pages = {6203-6212},
doi = {10.1039/d5fo01288k},
pmid = {40674041},
issn = {2042-650X},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Fermentation ; Feces/microbiology ; *Polysaccharides, Bacterial/metabolism/pharmacology ; Prebiotics ; Fatty Acids, Volatile/metabolism ; Bacteria/classification/genetics/isolation & purification/metabolism ; *Glycine max/metabolism ; *Soy Foods/microbiology/analysis ; Male ; Fermented Foods/microbiology ; Leuconostoc mesenteroides/metabolism ; Adult ; },
abstract = {The gut microbiome plays a key role in modulating human health and well-being. Exopolysaccharides (EPS) produced by lactic acid bacteria (LAB) are emerging as novel polymers that could exert a prebiotic effect via modification of this microbiome. Thus, incorporation of EPS to enhance food functionality is of interest. This study investigates the impact of a fermented soy beverage, supplemented with EPS produced by Leuconostoc mesenteroides DSA_O or DSA_F, on the faecal microbiota as assessed using an ex vivo model of the human distal colon. The soy beverage (SM) was prepared by fermentation with Lactiplantibacillus paraplantarum GB3 followed by supplementation with EPS_O (SMO) or EPS_F (SMF). Faecal samples from healthy donors were inoculated into a faecal fermentation medium with SM, SMO and SMF and incubated anaerobically at 37 °C for 24 h. After incubation, samples were subjected to shotgun metagenomic and short-chain fatty acid (SCFA) analysis. SMO and SMF were more effective than SM at enhancing the alpha diversity of the faecal microbiota after 24 h incubation. In addition, SMO promoted the growth of the health-associated species Bifidobacterium longum and Faecalibacterium prausnitzii, the latter of which is considered a next-generation probiotic. Butyrate and propionate levels were higher in faecal samples fermented with SMO and SMF than in SM. Taken together, these preliminary results indicate a potential role of EPS produced by Leuc. mesenteroides to be used as a functional food ingredient, modulating the gut microbiome as well as increasing the levels of SCFAs.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Fermentation
Feces/microbiology
*Polysaccharides, Bacterial/metabolism/pharmacology
Prebiotics
Fatty Acids, Volatile/metabolism
Bacteria/classification/genetics/isolation & purification/metabolism
*Glycine max/metabolism
*Soy Foods/microbiology/analysis
Male
Fermented Foods/microbiology
Leuconostoc mesenteroides/metabolism
Adult

@article {pmid40613821,
year = {2025},
author = {Saini, N and Ghosh, A and Bhadury, P},
title = {Linking plastic degradation potential and resistance gene abundance in bacterioplankton community of the Sundarbans estuarine ecosystem.},
journal = {FEMS microbiology letters},
volume = {372},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf067},
pmid = {40613821},
issn = {1574-6968},
support = {DST/SJF/E&ASA-01/2017-18//Science and Engineering Research Board/ ; },
mesh = {*Bacteria/genetics/classification/metabolism/isolation & purification ; *Plastics/metabolism ; Biodegradation, Environmental ; Estuaries ; *Plankton/genetics/metabolism/classification ; India ; *Microbiota/genetics ; Ecosystem ; Metagenomics ; },
abstract = {Harnessing microbial capabilities offers a promising and sustainable approach to address the global challenge of plastic waste. However, the potential of mangrove microbiomes to degrade diverse plastic polymers remains largely unexplored. In this metagenomic-based study, surface water microbiomes were analysed from the Indian Sundarbans, part of the world's largest contiguous mangrove ecosystem, revealing 748.21 hits per billion nucleotides associated with plastic-degrading enzymes (PDEs) targeting 17 different polymer types. Of these, 72.9% corresponded to synthetic polymers and 27.1% to natural polymers. The highest number of hits (223) was associated with polyethylene glycol-degrading enzymes, representing 26.7% of the total PDEs hits. Taxonomic analysis revealed Deltaproteobacteria and Gammaproteobacteria as key degraders of diverse synthetic plastic polymers, with Deltaproteobacteria emerging as a previously unreported group. This suggests that surface sediments may serve as reservoirs for novel plastic-degrading microbes. Co-occurrence network analysis indicated possible emerging co-selection or complex associations between PDEs, antibiotic resistance genes (ARGs), and metal resistance genes (MRGs). Notably, zinc resistance genes and aminoglycoside-related ARGs showed more associations with PDEs. While the presence of PDEs offers a promising avenue for bioremediation, their application may be complicated by the concurrent rise of ARGs and MRGs within PDE-harbouring microbes. Thus, it highlights the need for careful assessment when employing microbes for plastic bioremediation.},
}

*Bacteria/genetics/classification/metabolism/isolation & purification
*Plastics/metabolism
Biodegradation, Environmental
Estuaries
*Plankton/genetics/metabolism/classification
India
*Microbiota/genetics
Ecosystem
Metagenomics

@article {pmid40488951,
year = {2025},
author = {Liu, Y and Huang, G and Wei, F and Hu, Y},
title = {Non-negligible role of gut morphology in shaping mammalian gut microbiomes.},
journal = {Science China. Life sciences},
volume = {68},
number = {8},
pages = {2408-2419},
doi = {10.1007/s11427-024-2933-1},
pmid = {40488951},
issn = {1869-1889},
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Mammals/microbiology ; Bacteria/genetics/classification ; *Gastrointestinal Tract/microbiology/anatomy & histology ; Metagenomics/methods ; Metagenome ; },
abstract = {Because of the overemphasis on the roles of diet and phylogeny in shaping the gut microbiome, the gut morphology is seldom independently considered and even often ignored. To address this research gap, we investigated a large-scale dataset of mammalian gut microbiomes, comprising 16S ribosomal RNA and metagenomic sequencing data from 292 species spanning 20 orders. We dissected the effects of various factors on the gut microbiome across four distinct gut morphology categories (foregut/hindgut/simple, foregut/hindgut, functional ruminant/ruminant-like, and colon fermenter/cecum fermenter) and uncovered the synergistic effect between phylogeny and gut morphology. Moreover, we identified the significant role of gut morphology in the gut microbiomes of hosts occupying specific niches, as well as those within the same taxonomic order but with different gut morphologies. We also identified three enterotype indices-Fusobacterium, UCG-005, and Prevotella-which could predict the three gut morphology types of mammals: simple, foregut, and hindgut. These findings enhance our understanding of mammalian gut microbial assembly and provide novel insights into host-microbe coevolution.},
}

*Gastrointestinal Microbiome/genetics
Animals
Phylogeny
RNA, Ribosomal, 16S/genetics
*Mammals/microbiology
Bacteria/genetics/classification
*Gastrointestinal Tract/microbiology/anatomy & histology
Metagenomics/methods
Metagenome

@article {pmid39056464,
year = {2025},
author = {Czolk, R and Codreanu-Morel, F and de Nies, L and Busi, SB and Halder, R and Hunewald, O and Boehm, TM and Hefeng, FQ and De Beaufort, C and Wilmes, P and Ollert, M and Kuehn, A},
title = {Fecal IgE Analyses Reveal a Role for Stratifying Peanut-Allergic Patients.},
journal = {Journal of investigational allergology & clinical immunology},
volume = {35},
number = {4},
pages = {276-287},
doi = {10.18176/jiaci.1008},
pmid = {39056464},
issn = {1018-9068},
mesh = {Humans ; *Peanut Hypersensitivity/immunology/diagnosis ; *Feces/chemistry ; *Immunoglobulin E/immunology ; Female ; Male ; Child ; Allergens/immunology ; Child, Preschool ; Gastrointestinal Microbiome/immunology ; Arachis/immunology ; Cytokines/metabolism ; Adolescent ; },
abstract = {BACKGROUND AND OBJECTIVES: Peanut allergy (PA) is an IgE-mediated food allergy with variable clinical outcomes. Mild to-severe symptoms affect various organs and, often, the gastrointestinal tract. The role of intestine-derived IgE antibodies in gastrointestinal PA symptoms is poorly understood. Objective: This study aimed to examine fecal IgE responses in PA as a novel approach to patient endotyping.

METHODS: Feces and serum samples were collected from peanut-allergic and healthy children (n=26) to identify IgE and cytokines using multiplex assays. Shotgun metagenomics DNA sequencing and allergen database comparisons made it possible to identify microbial peptides with homology to known allergens.

RESULTS: Compared to controls, fecal IgE signatures showed broad diversity and increased levels for 13 allergens, including food, venom, contact, and respiratory allergens (P<.01-.0001). Overall, fecal IgE patterns were negatively correlated compared to sera IgE patterns in PA patients, with the greatest differences recorded for peanut allergens (P<.0001). For 83% of the allergens recognized by fecal IgE, we found bacterial homologs from PA patients' gut microbiome (eg, thaumatin-like protein Acinetobacter baumannii vs Act d 2, 109/124 aa identical). Compared to controls, PA patients had higher levels of fecal IgA, IL-22, and auto-IgE binding to their own fecal proteins (P<.001). Finally, levels of fecal IgE correlated with abdominal pain scores (P<.0001), suggesting a link between local IgE production and clinical outcomes.

CONCLUSIONS: Fecal IgE release from the intestinal mucosa could be an underlying mechanism of severe abdominal pain through the association between leaky gut epithelia and anticommensal TH2 responses in PA.},
}

Humans
*Peanut Hypersensitivity/immunology/diagnosis
*Feces/chemistry
*Immunoglobulin E/immunology
Female
Male
Child
Allergens/immunology
Child, Preschool
Gastrointestinal Microbiome/immunology
Arachis/immunology
Cytokines/metabolism
Adolescent

@article {pmid40713905,
year = {2025},
author = {Zhou, J and Zhang, CJ and Zou, D and Gu, C and Li, M},
title = {Magnetite drives microbial community restructuring and stimulates aceticlastic methanogenesis of type II Methanosarcina in mangrove sediments.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {174},
doi = {10.1186/s40168-025-02157-z},
pmid = {40713905},
issn = {2049-2618},
support = {42207144//National Natural Science Foundation of China/ ; 32225003, 32393971, and 32393970//National Natural Science Foundation of China/ ; 2024A1515010843//Guangdong Basic and Applied Basic Research Foundation/ ; 2023B0303000017//Guangdong Major Project of Basic and Applied Basic Research/ ; KCXFZ20240903092800002//Shenzhen Science and Technology Program/ ; 2022B002//Shenzhen University 2035 Program for Excellent Research/ ; },
mesh = {*Methane/metabolism/biosynthesis ; *Ferrosoferric Oxide/pharmacology/metabolism ; *Geologic Sediments/microbiology ; Wetlands ; *Methanosarcina/metabolism/genetics/classification/isolation & purification/drug effects ; *Microbial Consortia/drug effects ; *Microbiota/drug effects ; Acetates/metabolism ; Lactic Acid/metabolism ; },
abstract = {BACKGROUND: Mangrove wetlands are critical hotspots of methane emissions, yet the role of naturally occurring minerals in shaping their microbial communities and methanogenic processes is poorly understood. Magnetite, a common iron mineral in soils and sediments, has been reported to enhance aceticlastic methanogenesis and facilitate syntrophic methanogenesis. In this study, we integrated multi-omic profiling with cultivation-based approaches to investigate the impact of magnetite on methanogenesis of microbial consortia derived from mangrove sediments, using lactate as a substrate.

RESULTS: Across five serial transfers, mangrove microbial consortia converted lactate to propionate and acetate, which were subsequently degraded into methane. Magnetite addition significantly stimulated methane production, leading to notable changes in community structure, particularly for aceticlastic methanogens, with Methanosarcina predominating in the magnetite-amended cultures and Methanothrix in controls. Four Methanosarcina strains T3, T4, T13, and MeOH were subsequently isolated from magnetite-amended cultures. Combined analyses of metagenome-assembled genomes and the genomes of these isolates revealed that the enriched Methanosarcina in magnetite-amended cultures belonged to type II deficient in hydrogenotrophic methanogenesis pathway. Metatranscriptomic analyses suggested that magnetite addition stimulated aceticlastic methanogenesis of type II Methanosarcina and hydrogenotrophic methanogenesis of Methanomicrobiales in the consortia. Furthermore, pure culture experiments confirmed that magnetite stimulated aceticlastic methanogenesis by Methanosarcina sp. T3, although its gene expression patterns differed from those observed in the microbial consortia. Additionally, Methanofastidiosales, an uncultured archaeal lineage possessing H2-dependent methylotrophic methanogenesis, was detected in all transfers.

CONCLUSIONS: Our findings demonstrate that magnetite alters methanogenic consortia in mangrove sediments, selectively stimulating aceticlastic methanogenesis of type II Methanosarcina and modulating hydrogenotrophic activity in Methanomicrobiales. By integrating multi-omics analyses with pure culture validation, we demonstrate, for the first time, that magnetite directly enhances the aceticlastic methanogenesis of type II non-hydrogenotrophic Methanosarcina. This study provides new insights into the influence of magnetite on complex microbial consortia, offers a deeper understanding of the physiology of type II non-hydrogenotrophic Methanosarcina, and advances knowledge of mineral-mediated regulation of methanogenic networks in anoxic environments. Video Abstract.},
}

*Methane/metabolism/biosynthesis
*Ferrosoferric Oxide/pharmacology/metabolism
*Geologic Sediments/microbiology
Wetlands
*Methanosarcina/metabolism/genetics/classification/isolation & purification/drug effects
*Microbial Consortia/drug effects
*Microbiota/drug effects
Acetates/metabolism
Lactic Acid/metabolism

@article {pmid40713701,
year = {2025},
author = {Bhardwaj, K and Niharika, and Garg, A and Jain, A and Kumar, M and Datt, M and Singh, V and Vrati, S},
title = {Identification and profiling of novel metagenome assembled uncultivated virus genomes from human gut.},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {254},
pmid = {40713701},
issn = {1743-422X},
support = {BT/PR18657/BIC/101/507/2016//Department of Biotechnology, Ministry of Science and Technology, India/ ; JCB/2021/000015//Science and Engineering Research Board/ ; },
mesh = {Humans ; *Genome, Viral ; *Metagenome ; Feces/virology ; *Virome ; Metagenomics ; *Gastrointestinal Tract/virology ; *Viruses/genetics/classification/isolation & purification ; Gastrointestinal Microbiome ; Phylogeny ; },
abstract = {Metagenomics has revealed an unprecedented viral diversity in human gut although, most of the sequence data remains uncharacterized. In this study, we mined a collection of 1090 metagenome assembled "high quality" viral genomes (> 90% completeness, as determined by CheckV) derived from human fecal samples. Sequence analysis revealed eight new species spanning seven genera within the class, Caudoviricetes and nineteen new species from fourteen genera within the ssDNA virus family, Microviridae. Additionally, four "high quality" genomes were not found in any of the four major viral databases, NCBI viral RefSeq, IMG-VR, Gut Phage Database (GPD) and Gut Virome Database (GVD). Further, annotation and KEGG pathway analysis of the "high-quality" genomes identified seven core genes (antB, dnaB, DNMT1, DUT, xlyAB, xtmB and xtmA) associated with metabolism and fundamental viral processes. Moreover, genes for virulence, host-takeover, drug resistance, tRNA, tmRNA and CRISPR elements were also detected. Host prediction analysis suggest bacterial hosts for approximately 40% of the genomes. Overall, this study reports the discovery of novel viral genomes and provides a comprehensive genome profiling of human gut viruses in a subpopulation from India. These findings serve as a foundation for future biological investigations to elucidate the role of these viruses in host physiology.},
}

Humans
*Genome, Viral
*Metagenome
Feces/virology
*Virome
Metagenomics
*Gastrointestinal Tract/virology
*Viruses/genetics/classification/isolation & purification
Gastrointestinal Microbiome
Phylogeny

@article {pmid40711892,
year = {2025},
author = {Turner, D and Adriaenssens, EM and Amann, RI and Bardy, P and Bartlau, N and Barylski, J and Błażejak, S and Bouzari, M and Briegel, A and Briers, Y and Carrillo, D and Chen, X and Claessen, D and Cook, R and Crisci, MA and Dechesne, A and Deptula, P and Dutilh, BE and Ely, B and Fieseler, L and Fogg, PCM and Fukudome, A and Ganjoor, MS and Gientka, I and Holmfeldt, K and Kalatzis, PG and Kauffman, KM and Kempff, A and Knezevic, P and Koonin, EV and Kropinski, AM and Krupovic, M and Kurtböke, I and Lambon, K and Lavigne, R and Lehman, SM and Liu, HT and Lood, C and Lurz, R and Mäntynen, S and Matrishin, CB and Middelboe, M and Millard, AD and Moraru, C and Nielsen, DS and Nobrega, FL and Nunoura, T and Oksanen, HM and Ongenae, V and Parra, B and Pas, C and Pogliano, J and Poranen, MM and Potipimpanon, S and Prichard, A and Pye, HV and Rothschild-Rodriguez, D and Rozen, DE and Santini, JM and Sha, Y and Shymialevich, D and Sokołowska, B and Soleimani-Delfan, A and Średnicka, P and Tavares, P and Telatin, A and Tolstoy, I and Urayama, SI and van Neer, V and Vogensen, FK and Wen, Q and Wichels, A and Wójcicki, M and Ictv Taxonomy Summary Consortium, and Ictv Taxonomy Summary Consortium, and , },
title = {Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses (ICTV) from the Bacterial Viruses Subcommittee, 2025.},
journal = {The Journal of general virology},
volume = {106},
number = {7},
pages = {},
doi = {10.1099/jgv.0.002111},
pmid = {40711892},
issn = {1465-2099},
mesh = {*Viruses/classification/genetics ; *Bacteria/virology ; Phylogeny ; *Classification/methods ; },
abstract = {This article summarises the activities of the International Committee on Taxonomy of Viruses Bacterial Viruses Subcommittee, detailing developments in the classification of bacterial viruses. We provide here an overview of all new, abolished, moved and renamed taxa proposed in 2024, approved by the Executive Committee, and ratified by membership vote in 2025. Through the collective efforts of 74 international contributors of taxonomy proposals in this round, 43 ratified proposals have led to the creation of one new phylum, one class, four orders, 33 families, 14 subfamilies, 194 genera and 995 species. These proposals mark significant progress in refining the taxonomy of bacterial viruses. Key updates include the creation of new orders and families that include existing taxa to better reflect genomic and evolutionary relationships. As sequencing and bioinformatics approaches continue to advance, further expansion and refinements in viral taxonomy can be anticipated in the coming years.},
}

*Viruses/classification/genetics
*Bacteria/virology
Phylogeny
*Classification/methods

@article {pmid40516324,
year = {2025},
author = {Xu, R and Li, T and Wang, Z and Wang, H and Sun, M and Xie, J and Tong, L and Peng, W and Wang, Y},
title = {Association among lean mass, gut microbiome alterations and bone mineral density in high-altitude.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {51},
number = {},
pages = {18-27},
doi = {10.1016/j.clnu.2025.05.018},
pmid = {40516324},
issn = {1532-1983},
mesh = {Humans ; *Bone Density/physiology ; *Altitude ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Middle Aged ; Absorptiometry, Photon ; Adult ; *Body Composition/physiology ; Body Mass Index ; Tibet ; Feces/microbiology ; Lumbar Vertebrae ; },
abstract = {BACKGROUND: Body composition, particularly lean body mass, plays a pivotal role in skeletal health and has been increasingly linked to the gut microbiota (GM). However, evidence from vulnerable high-altitude populations remains scarce.

OBJECTIVE: This study aimed to evaluate the association between body composition and bone mineral density (BMD) at high altitudes and explore the potential role of GM.

METHODS: A total of 820 Tibetan participants were recruited. BMD at the lumbar spine (L1-L4) and total hip was measured using dual-energy X-ray absorptiometry (DXA). Multivariate linear regression was applied to evaluate the associations between body composition indices and BMD. Participants were stratified into low lean mass index (LLMI) and high lean mass index (HLMI) subgroups using restricted cubic splines (RCS) and body mass index. Stool samples from a subset of participants (n = 383) were analyzed to determine the relative abundances of KEGG Orthology groups.

RESULTS: LMI was positively associated with hip BMD at high altitude [β (95 % CI) = 0.005 (0.003,0.007), P < 0.05], whereas no significant association was observed with spine BMD. This correlation varied significantly by altitude (Pinter< 0.05). A similar positive relationship was observed between microbial diversity (Shannon index) and hip_BMD [hip: β (95 % CI) = 0.605 (0.165, 1.044), P < 0.05]. Compared to the HLMI group, LLMI participants exhibited greater microbial diversity (P < 0.05), higher Faecalibacteriums abundance, and lower levels of Prevotella copri (P< 0.05). Functional metagenomic analysis identified differential enrichment of microbial pathways, including riboflavin metabolism, terpenoid backbone biosynthesis, alanine, aspartate, and glutamate metabolism (P < 0.05).

CONCLUSION: These findings highlight the correlation between LMI and hip BMD among high-altitude Tibetan adults, offering a potential mechanism for the interplay between GM profiles and bone health in high-altitude populations.},
}

Humans
*Bone Density/physiology
*Altitude
*Gastrointestinal Microbiome/physiology
Male
Female
Middle Aged
Absorptiometry, Photon
Adult
*Body Composition/physiology
Body Mass Index
Tibet
Feces/microbiology
Lumbar Vertebrae

@article {pmid40348632,
year = {2025},
author = {Lotankar, M and Houttu, N and Benchraka, C and Lahti, L and Laitinen, K},
title = {Links between gut microbiota with specific serum metabolite groups in pregnant women with overweight or obesity.},
journal = {Nutrition, metabolism, and cardiovascular diseases : NMCD},
volume = {35},
number = {9},
pages = {104095},
doi = {10.1016/j.numecd.2025.104095},
pmid = {40348632},
issn = {1590-3729},
mesh = {Adult ; Female ; Humans ; Pregnancy ; Young Adult ; *Bacteria/metabolism/genetics/classification ; Biomarkers/blood ; Cross-Sectional Studies ; Feces/microbiology ; *Gastrointestinal Microbiome ; Magnetic Resonance Spectroscopy ; *Metabolome ; *Metabolomics/methods ; Metagenomics ; *Obesity/diagnosis/microbiology/blood ; *Pregnancy Complications/blood/diagnosis/microbiology ; Randomized Controlled Trials as Topic ; Multicenter Studies as Topic ; },
abstract = {BACKGROUND AND AIM: Gut microbiota may regulate metabolism but is incompletely characterized in pregnancy. Our objective was to investigate the relations using omics techniques.

METHODS AND RESULTS: In a cross-sectional setting, fecal and serum samples of 361 healthy pregnant women with overweight or obesity were analyzed with a combinatorial approach of metagenomics and targeted NMR-based metabolomics, with statistical and machine learning techniques to identify and analyze the extent to which the gut microbiota composition and predicted functions would be reflected in the serum metabolome. We identified five biclusters, each of which consisted of a set of gut microbial species and serum metabolites with correlated abundance profiles. Two of the biclusters included metabolites that have been linked to the cardiovascular health; one was linked with factors known to increase the risk i.e., various sizes of lipoprotein subclasses (VLDL and LDL), subclasses of relative lipoprotein lipid concentrations (VLDL, IDL, and LDL), apolipoprotein B, and an inflammation marker, glycoprotein acetylation. These metabolites were associated with abundances of species such as, Enterocloster bolteae and Ruminococcus gnavus. The second bicluster included metabolites linked with a reduced cardiovascular risk, such as different sizes of HDL (high-density lipoprotein), subclasses for relative lipoprotein lipid concentrations and mean diameter for HDL particles, and fatty acid ratios. These metabolites were associated with abundances of species, such as Bacteroides cellulosilyticus and Alistipes finegoldii. We did not observe any biclusters between predicted pathways and serum metabolites.

CONCLUSION: Overall, we identified five biclusters of co-abundant gut bacteria and serum metabolites , of which two were linked to pro-atherogenic and anti-atherogenic properties.

TRIAL REGISTRATION: www.

CLINICALTRIALS: Gov: NCT01922791.},
}

Adult
Female
Humans
Pregnancy
Young Adult
*Bacteria/metabolism/genetics/classification
Biomarkers/blood
Cross-Sectional Studies
Feces/microbiology
*Gastrointestinal Microbiome
Magnetic Resonance Spectroscopy
*Metabolome
*Metabolomics/methods
Metagenomics
*Obesity/diagnosis/microbiology/blood
*Pregnancy Complications/blood/diagnosis/microbiology
Randomized Controlled Trials as Topic
Multicenter Studies as Topic

@article {pmid40311618,
year = {2025},
author = {Andreu-Sánchez, S and Blanco-Míguez, A and Wang, D and Golzato, D and Manghi, P and Heidrich, V and Fackelmann, G and Zhernakova, DV and Kurilshikov, A and Valles-Colomer, M and Weersma, RK and Zhernakova, A and Fu, J and Segata, N},
title = {Global genetic diversity of human gut microbiome species is related to geographic location and host health.},
journal = {Cell},
volume = {188},
number = {15},
pages = {3942-3959.e9},
doi = {10.1016/j.cell.2025.04.014},
pmid = {40311618},
issn = {1097-4172},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Genetic Variation ; Phylogeny ; Metagenome/genetics ; Male ; Female ; Bile Acids and Salts/blood ; Clostridiales ; },
abstract = {The human gut harbors thousands of microbial species, each exhibiting significant inter-individual genetic variability. Although many studies have associated microbial relative abundances with human-health-related phenotypes, the substantial intraspecies genetic variability of gut microbes has not yet been comprehensively considered, limiting the potential of linking such genetic traits with host conditions. Here, we analyzed 32,152 metagenomes from 94 microbiome studies across the globe to investigate the human microbiome intraspecies genetic diversity. We reconstructed 583 species-specific phylogenies and linked them to geographic information and species' horizontal transmissibility. We identified 484 microbial-strain-level associations with 241 host phenotypes, encompassing human anthropometric factors, biochemical measurements, diseases, and lifestyle. We observed a higher prevalence of a Ruminococcus gnavus clade in nonagenarians correlated with distinct plasma bile acid profiles and a melanoma and prostate-cancer-associated Collinsella clade. Our large-scale intraspecies genetic analysis highlights the relevance of strain diversity as it relates to human health.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Genetic Variation
Phylogeny
Metagenome/genetics
Male
Female
Bile Acids and Salts/blood
Clostridiales

@article {pmid39662692,
year = {2025},
author = {Costigan, CM and Warren, FJ and Duncan, AP and Hoad, CL and Lewis, N and Hill, T and Crooks, CJ and Morgan, PS and Ciacci, C and Iovino, P and Sanders, DS and Hildebrand, F and Gowland, PA and Spiller, RC and Marciani, L},
title = {One Year of Gluten-Free Diet Impacts Gut Function and Microbiome in Celiac Disease.},
journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association},
volume = {23},
number = {9},
pages = {1525-1534.e14},
doi = {10.1016/j.cgh.2024.11.006},
pmid = {39662692},
issn = {1542-7714},
mesh = {Humans ; *Celiac Disease/diet therapy/pathology ; Male ; Female ; *Diet, Gluten-Free/methods ; Adult ; Feces/microbiology ; Middle Aged ; *Gastrointestinal Microbiome ; Cohort Studies ; Young Adult ; Magnetic Resonance Imaging ; Metagenomics ; },
abstract = {BACKGROUND & AIMS: Currently, the main treatment for celiac disease (CD) is the gluten-free diet (GFD). This observational cohort study investigated the impact of CD and 1 year of GFD on gut function and microbiome.

METHODS: A total of 36 newly diagnosed patients and 36 healthy volunteers (HVs) were studied at baseline and at 12-month follow-up. Small bowel water content (SBWC), whole gut transit time (WGTT), and colon volumes were measured by magnetic resonance imaging. Stool sample DNA was subjected to shotgun metagenomic sequencing. Species-level abundances and gene functions, including CAZymes (carbohydrate active enzymes) were determined.

RESULTS: SBWC was significantly higher in people with CD (157 ± 15 mL) vs (HVs 100 ± 12 mL) (P = .003). WGTT was delayed in people with CD (68 ± 8 hours) vs HVs (41 ± 5 hours) (P = .002). The differences reduced after 12 months of GFD but not significantly. Well-being in the CD group significantly improved after GFD but did not recover to control values. CD fecal microbiota showed a high abundance of proteolytic gene functions, associated with Escherichia coli, Enterobacter, and Peptostreptococcus. GFD significantly reduced Bifidobacteria and increased Blautia wexlerae. Microbiome composition correlated positively with WGTT, colonic volume, and Akkermansia municphilia but negatively with B wexerelae. Following GFD, the reduction in WGTT and colonic volume was significantly associated with increased abundance of B wexlerae. There were also significant alterations in CAZyme profiles, specifically starch- and arabinoxylan-degrading families.

CONCLUSIONS: CD impacted gut function and microbiota. GFD ameliorated but did not reverse these effects, significantly reducing Bifidobacteria associated with reduced intake of resistant starch and arabinoxylan from wheat.

CLINICALTRIALS: gov, number: NCT02551289.},
}

Humans
*Celiac Disease/diet therapy/pathology
Male
Female
*Diet, Gluten-Free/methods
Adult
Feces/microbiology
Middle Aged
*Gastrointestinal Microbiome
Cohort Studies
Young Adult
Magnetic Resonance Imaging
Metagenomics

@article {pmid40707990,
year = {2025},
author = {Drevland, OM and de Muinck, EJ and Trosvik, P and Hammerstad, M and Kvitne, KE and Midtvedt, K and Åsberg, A and Robertsen, I},
title = {Microbiome-derived reactivation of mycophenolate explains variations in enterohepatic recirculation in kidney transplant recipients.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {169},
pmid = {40707990},
issn = {2049-2618},
support = {315792//Norges Forskningsråd/ ; 315792//Norges Forskningsråd/ ; },
mesh = {*Mycophenolic Acid/pharmacokinetics/analogs & derivatives/metabolism ; *Kidney Transplantation ; Humans ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; *Immunosuppressive Agents/pharmacokinetics/therapeutic use ; Middle Aged ; Feces/microbiology ; Adult ; Transplant Recipients ; Glucuronidase/metabolism/genetics ; Glucuronides/metabolism ; Metagenomics/methods ; *Enterohepatic Circulation ; },
abstract = {BACKGROUND: The pivotal role of microbes in drug metabolism is increasingly recognized, as variation in the gut microbiome composition between individuals has been shown to impact systemic drug exposure, efficacy and toxicity. Mycophenolate mofetil (MMF) is a cornerstone in immunosuppressive therapy following solid organ transplantation. However, dosing and tolerance are challenged by significant pharmacokinetic variability among patients, largely due to variable degrees of enterohepatic recirculation of mycophenolic acid (MPA), the active moiety of MMF. It is hypothesized that the variability in MPA recirculation is driven by gut microbiome-derived β-glucuronidase (β-GUS) mediated cleavage of MPA-glucuronide (MPAG) excreted in the bile. Here, we investigated the bidirectional interaction between MPA and the gut microbiome in kidney transplant recipients, using a combination of in vivo and in vitro data.

RESULTS: We compared the fecal microbiomes of kidney transplant recipients (n = 21) both pre- and post-transplantation to healthy individuals (n = 15) using shotgun metagenomic sequencing. We also determined the individual microbiome-derived reactivation rate of MPAG to MPA and show a strong positive correlation between this reactivation rate and the degree of MPA enterohepatic recirculation in vivo. Through metagenomic analysis, the reactivation rate of MPA was linked to specific gut microbial species. In particular, specific β-GUS gene variants associated with Faecalibacterium prausnitzii showed a strong impact on the conversion of MPAG to MPA. Furthermore, our study confirmed a significant shift in microbial composition post-transplantation and revealed notable fluctuations in species such as F. prausnitzii and Akkermansia muciniphila across different time points after transplantation. Lastly, we provide evidence that the microbiome-derived reactivation rate of MPA is linked to specific beta-glucuronidase alleles.

CONCLUSIONS: We highlight for the first time that the ex vivo determined reactivation rate of MPA explains the variation of enterohepatic recirculation, emphasizing the important role of F. prausnitzii in this process. More broadly, our findings suggest that the gut microbiome significantly influences the degree of enterohepatic recirculation of MPA, providing valuable insights that could be relevant for optimizing individualized immunosuppressive drug dosing in transplant patients. Video Abstract.},
}

*Mycophenolic Acid/pharmacokinetics/analogs & derivatives/metabolism
*Kidney Transplantation
Humans
*Gastrointestinal Microbiome/drug effects
Male
Female
*Immunosuppressive Agents/pharmacokinetics/therapeutic use
Middle Aged
Feces/microbiology
Adult
Transplant Recipients
Glucuronidase/metabolism/genetics
Glucuronides/metabolism
Metagenomics/methods
*Enterohepatic Circulation

@article {pmid40707831,
year = {2025},
author = {Sereika, M and Mussig, AJ and Jiang, C and Knudsen, KS and Jensen, TBN and Petriglieri, F and Yang, Y and Jørgensen, VR and Delogu, F and Sørensen, EA and Nielsen, PH and Singleton, CM and Hugenholtz, P and Albertsen, M},
title = {Genome-resolved long-read sequencing expands known microbial diversity across terrestrial habitats.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40707831},
issn = {2058-5276},
support = {130690//Villum Fonden (Villum Foundation)/ ; 50093//Villum Fonden (Villum Foundation)/ ; },
abstract = {The emergence of high-throughput, long-read DNA sequencing has enabled recovery of microbial genomes from environmental samples at scale. However, expanding the terrestrial microbial genome catalogue has been challenging due to the enormous complexity of these environments. Here we performed deep, long-read Nanopore sequencing of 154 soil and sediment samples collected during the Microflora Danica project, yielding genomes of 15,314 previously undescribed microbial species, recovered using our custom mmlong2 workflow. The recovered microbial genomes span 1,086 previously uncharacterized genera and expand the phylogenetic diversity of the prokaryotic tree of life by 8%. The long-read assemblies also enabled the recovery of thousands of complete ribosomal RNA operons, biosynthetic gene clusters and CRISPR-Cas systems. Furthermore, the incorporation of the recovered genomes into public genomic databases substantially improved species-level classification rates for soil and sediment metagenomic datasets. These findings demonstrate that long-read sequencing allows cost-effective recovery of high-quality microbial genomes from highly complex ecosystems, which remain an untapped source of biodiversity.},
}

@article {pmid40645041,
year = {2025},
author = {Pei, J and Chen, S and Yu, K and Liang, J and Zhang, R and Li, P and Hou, Z and Fu, L and Ma, H},
title = {Microbial regulation of dissolved organic matter revealed by integrated metabolomics and metagenomics in the World's deepest blue hole.},
journal = {Marine environmental research},
volume = {210},
number = {},
pages = {107354},
doi = {10.1016/j.marenvres.2025.107354},
pmid = {40645041},
issn = {1879-0291},
mesh = {Metagenomics ; Metabolomics ; *Microbiota ; Nitrogen/analysis ; Seawater/microbiology/chemistry ; China ; *Environmental Monitoring ; Sulfur/analysis ; *Water Microbiology ; },
abstract = {Dissolved organic matter (DOM) is central to marine biogeochemical cycles, with its composition and dynamics closely linked to microbial communities. In oxygen-stratified extreme environments, however, the ecological relationships between DOM and microbes remain insufficiently explored. This study explores the dynamics of DOM and microbial communities in the Sansha Yongle Blue Hole, the world's deepest ocean blue hole, using an integrated metabolomics and metagenomics approach. Our findings elucidate significant alterations in microbial communities and DOM composition in response to variations in oxygen concentrations. Specifically, various DOM components, including dissolved organic sulfur (DOS) and dissolved organic nitrogen (DON), along with a spectrum of small molecule metabolites, were affected by microbial metabolic activities. Higher concentrations of DOS in the anoxic layer were positively correlated with increased sulfur metabolism in microbial communities, whereas lower concentrations of DON in the chemocline were associated with the coupling of nitrification and denitrification processes. Additionally, metabolites such as lipids, amino acids, isovalerylcarnitine, and peptides, associated with microbial physiological functions, energy metabolism, and signal transduction processes, varied with oxygen stratification. These findings contribute to a deeper understanding of the intricate relationships between microbial communities and DOM dynamics in extreme marine environments.},
}

Metagenomics
Metabolomics
*Microbiota
Nitrogen/analysis
Seawater/microbiology/chemistry
China
*Environmental Monitoring
Sulfur/analysis
*Water Microbiology

@article {pmid40582136,
year = {2025},
author = {Song, L and Hu, C and Zhang, X and Liu, Y and Song, G and Wu, J and Wang, Z and Sun, M},
title = {Effects of feeding on microbial community structure and pathogen abundance in marine aquaculture ponds.},
journal = {Marine environmental research},
volume = {210},
number = {},
pages = {107319},
doi = {10.1016/j.marenvres.2025.107319},
pmid = {40582136},
issn = {1879-0291},
mesh = {*Aquaculture ; *Ponds/microbiology ; *Microbiota ; Eutrophication ; Bacteria ; *Water Microbiology ; Water Quality ; Animals ; },
abstract = {Microbial communities in aquaculture ponds play a vital role in regulating water quality, driving nutrient cycling, and maintaining ecological balance. In 2023, we conducted a study to evaluate how feeding affects microbial communities by comparing the microbial composition and water quality in both fed and unfed aquaculture ponds. Metagenomic sequencing indicated that feeding significantly elevated the relative abundance of bacteria within the microbial community. Ecological similarity analysis showed that bacterial community in the ponds predominantly originated from internal pond sources, rather than from adjacent coastal waters. Furthermore, the relative abundance of pathogenic bacteria was significantly higher in fed ponds, with Vibrio parahaemolyticus levels reaching 1.6 times those in unfed ponds. In addition, water quality assessments further showed that feeding elevated nutrient concentrations, leading to eutrophication. Analyses of redundancy and correlation showed a notable positive link (p < 0.05) between the levels of pathogenic bacteria and the concentration of organic nutrients. These results suggest that excessive feeding contributes to eutrophication, which promotes the growth of bacteria, including pathogenic strains, thereby increasing the risk of disease outbreaks in aquaculture systems.},
}

*Aquaculture
*Ponds/microbiology
*Microbiota
Eutrophication
Bacteria
*Water Microbiology
Water Quality
Animals

@article {pmid40532529,
year = {2025},
author = {Parab, AS and Ghose, M and Manohar, CS},
title = {Metagenomic reconstruction of microbial genomes and biogeochemical pathways: insights into carbon and nitrogen flux dynamics in the eastern Arabian Sea.},
journal = {Marine environmental research},
volume = {210},
number = {},
pages = {107292},
doi = {10.1016/j.marenvres.2025.107292},
pmid = {40532529},
issn = {1879-0291},
mesh = {Nitrogen/metabolism/analysis ; Seawater/microbiology/chemistry ; *Nitrogen Cycle ; Metagenomics ; Carbon/metabolism ; *Metagenome ; Bacteria/genetics ; *Carbon Cycle ; *Genome, Microbial ; Seasons ; Microbiota ; },
abstract = {The eastern Arabian Sea (EAS) experiences seasonal nutrient availability and productivity shifts driven by the Indian monsoon, influencing microbial contributions to biogeochemical cycles. This study explores carbon, nitrogen and sulfur cycling using metagenome-assembled genomes (MAGs) from water samples collected at chlorophyll maxima (C-Max) depths during non-monsoon and monsoon seasons. A total of 49 high-quality MAGs were reconstructed from 12 metagenomic samples, including four novel lineages from the phyla Pseudomonadota and Bacteroidota. These MAGs revealed distinct seasonal shifts in microbial composition and function. During the non-monsoon season, microbial communities dominated by Idiomarina and Marinobacter showed increased gene abundance for C1 compound metabolism, nitrogen cycling and sulfur oxidation, processes essential for managing climate-active gases such as carbon dioxide (CO2) and nitrous oxide (N2O), while also preventing toxic sulfide accumulation. In contrast, monsoon conditions enhanced organic matter influx, promoting nitrogen retention pathways driven by Sinimarinibacterium and Oleibacter, raising concerns about potential nutrient buildup and localized hypoxia. Despite seasonal variations, functional redundancy ensured the stability of nutrient cycling processes. PERMANOVA analysis (p < 0.001) confirmed that microbial functional gene distribution was primarily shaped by taxonomic structure, with genus-level composition playing a dominant role. The study highlights microbial adaptability and resilience, ensuring ecosystem stability in the dynamic EAS environment. Understanding microbial processes at C-Max depths has enhanced our understanding of biogeochemical cycling in the EAS. Although focused on oxygenated depths, these findings offer insights relevant to microbial functions in the OMZ, reflecting the distinct environmental conditions of EASs.},
}

Nitrogen/metabolism/analysis
Seawater/microbiology/chemistry
*Nitrogen Cycle
Metagenomics
Carbon/metabolism
*Metagenome
Bacteria/genetics
*Carbon Cycle
*Genome, Microbial
Seasons
Microbiota

@article {pmid40398297,
year = {2025},
author = {Shen, Y and Li, Y and Xiao, J and Li, J and Wu, Y and Wu, Y and Tang, H and Fang, X and Wang, L and Gong, Y and Chen, H and Yan, X},
title = {Comparative microbiomic analysis of fecal microbiota associated with abdominal fat in ducks.},
journal = {Poultry science},
volume = {104},
number = {8},
pages = {105282},
pmid = {40398297},
issn = {1525-3171},
mesh = {Animals ; *Ducks/microbiology/physiology ; *Gastrointestinal Microbiome ; *Abdominal Fat/physiology ; Adiposity ; Meat ; Feces ; *Bacteria/classification/genetics/isolation & purification ; Female ; },
abstract = {The gut microbiota, which features complex community structures, colonizes the duck intestine and plays a crucial role in metabolism, immune regulation, and meat quality. Gut-microbiota-regulated abdominal fat deposition is a key factor that affects the meat quality of livestock and poultry. We used 16S rDNA and metagenomic sequencing to investigate the microbial community characteristics of 187 fecal samples from 10 Chinese indigenous duck breeds (five breeds for each of the high/low abdominal fat categories). We explored the relationship between fecal microbiota and abdominal fat deposition. The α diversity of the fecal microbiome in high abdominal fat ducks (HAF) was higher than that in low abdominal fat ducks (LAF). The fecal microbiota and function were also significantly different. At the phylum level, Actinobacteria was significantly enriched in HAF, whereas Proteobacteria, Candidatus, Saccharibacteria, and Fusobacteria were abundant in LAF. At the genus level, Lactobacillus, Alistipes, Corynebacterium, and Lachnoclostridium were more abundant in HAF than in LAF. The Streptococcus, Campylobacter, Helicobacter, Enterobacter, Gallibacterium, and Escherichia genera were significantly enriched in LAF. Microbial functional analysis indicated that the HAF fecal microbiota was mainly involved in carbohydrate, nucleotide, lipid, amino acid, terpenoids, polyketides, and xenobiotic metabolism. In addition, bacteria related to signal transduction, cofactor and vitamin metabolism, and infectious disease were enriched in LAF. This study revealed the relationship between gut microbiota and abdominal fat deposition in ducks. Our findings lay a foundation for the abdominal fat deposition mechanism in ducks and provide a reference for Chinese indigenous duck husbandry.},
}

Animals
*Ducks/microbiology/physiology
*Gastrointestinal Microbiome
*Abdominal Fat/physiology
Adiposity
Meat
Feces
*Bacteria/classification/genetics/isolation & purification
Female

@article {pmid40135776,
year = {2025},
author = {Wang, J and Liu, Q and Jin, S and Yang, B and Wang, C and Tan, Y and Feng, W and Tao, J and Wang, H and Wang, Y and Yang, S and Cui, L},
title = {Characterization of Bile Microbiota in Patients With Obstructive Jaundice Associated With Biliary Tract Diseases.},
journal = {Clinical and translational gastroenterology},
volume = {16},
number = {7},
pages = {e00841},
doi = {10.14309/ctg.0000000000000841},
pmid = {40135776},
issn = {2155-384X},
support = {62071011，81800604, 2023YFC2413802//National Natural Science Foundation of China, Key Clinical Specialty Funding Project of Beijin, Hospital-Enterprise Joint Funding Project, National Key Research and Development Program/ ; },
mesh = {Humans ; *Jaundice, Obstructive/microbiology/diagnosis/etiology ; Male ; *Bile/microbiology/chemistry ; Female ; Middle Aged ; Aged ; RNA, Ribosomal, 16S/genetics ; *Gallstones/microbiology/complications ; *Microbiota/genetics ; *Bacteria/isolation & purification/genetics/classification ; Metagenomics ; *Cholangiocarcinoma/microbiology/complications/diagnosis ; Biomarkers/analysis ; *Bile Duct Neoplasms/microbiology/complications/diagnosis ; Adult ; High-Throughput Nucleotide Sequencing ; Constriction, Pathologic/microbiology ; },
abstract = {INTRODUCTION: Cholangiocarcinoma (CHOL), a malignant tumor of the biliary system, is particularly concerning because of its high malignancy and poor prognosis, often leading to obstructive jaundice. The advent of metagenomic next-generation sequencing technology has expanded diagnostic capabilities, including the identification of microbes within tumors and their potential role in cancer progression. The aims of this study were to explore the bacterial composition in bile from patients with obstructive jaundice of different etiologies and to investigate the association between bile microbiota and biochemical analytes, as well as their potential as biomarkers for diagnosis of obstructive jaundice diseases.

METHODS: Bile samples from patients with obstructive jaundice admitted to Beijing Friendship Hospital were collected and subjected to 16S rRNA and metagenomic sequencing. The study included patients diagnosed with benign biliary stricture, gallstone, and CHOL. Clinical data and bile chemical components were analyzed. The potential functional roles of the identified microbiota were predicted using bioinformatics tools.

RESULTS: The study enrolled 13 patients with benign biliary stricture, 19 with gallstones, and 10 with CHOL. Significant differences in bile chemical components and microbial diversity were observed among the groups. The bile microbiota was dominated by distinct phyla and genera across the groups, with Proteobacteria and Fusobacteriota enriched in benign biliary stricture, Firmicutes and Desulfobacterota in CHOL, and Synergistota in patients with gallstone. Functional analysis revealed differences in gene functions related to metabolism and other biological processes. A correlation between bile microbiota and biochemical markers was established, and the combination of differential microbiota showed potential as a diagnostic marker for obstructive jaundice of different etiologies.

DISCUSSION: Bile microbiota varies significantly among patients with obstructive jaundice of different etiologies. The identified microbial signatures and their functional roles could serve as novel diagnostic markers and provide insights into the pathogenesis of biliary diseases.},
}

Humans
*Jaundice, Obstructive/microbiology/diagnosis/etiology
Male
*Bile/microbiology/chemistry
Female
Middle Aged
Aged
RNA, Ribosomal, 16S/genetics
*Gallstones/microbiology/complications
*Microbiota/genetics
*Bacteria/isolation & purification/genetics/classification
Metagenomics
*Cholangiocarcinoma/microbiology/complications/diagnosis
Biomarkers/analysis
*Bile Duct Neoplasms/microbiology/complications/diagnosis
Adult
High-Throughput Nucleotide Sequencing
Constriction, Pathologic/microbiology

@article {pmid40119849,
year = {2025},
author = {Riva, A and Sahin, E and Volpedo, G and Catania, NT and Venara, I and Biagioli, V and Balagura, G and Amadori, E and De Caro, C and Cerulli Irelli, E and Di Bonaventura, C and Zara, F and Sezerman, OU and Russo, E and Striano, P},
title = {Medication-resistant epilepsy is associated with a unique gut microbiota signature.},
journal = {Epilepsia},
volume = {66},
number = {7},
pages = {2268-2284},
doi = {10.1111/epi.18367},
pmid = {40119849},
issn = {1528-1167},
support = {MDBR-23-004-STXBP1//Fingerprinting a multiomics biomarker profile in patients with STXBP1-RD/ ; PNRR-MUR-M4C2 PE0000006//MNESYS/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Child ; *Drug Resistant Epilepsy/microbiology/drug therapy ; Child, Preschool ; Adolescent ; Anticonvulsants/therapeutic use ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Cohort Studies ; },
abstract = {OBJECTIVE: Dysfunction of the microbiota-gut-brain axis is emerging as a new pathogenic mechanism in epilepsy, potentially impacting on medication response and disease outcome. We investigated the composition of the gut microbiota in a cohort of medication-resistant (MR) and medication-sensitive (MS) pediatric patients with epilepsy.

METHODS: Children with epilepsy of genetic and presumed genetic etiologies were evaluated clinically and subgrouped into MR and MS. Age-matched healthy controls (HCs) were also recruited. A food diary was used to evaluate nutritional habits, and the Rome IV questionnaire was used to record gastrointestinal symptoms. The microbiota composition was assessed in stool samples through 16S rRNA. α-Diversity (AD) and β-diversity (BD) were calculated, and differential abundance analysis was performed using linear multivariable models (significance: p.adj < .05).

RESULTS: Forty-one patients (MR:MS = 20:21) with a mean age of 7.2 years (±4.6 SD) and 27 age-matched HCs were recruited. No significant differences in AD were found when comparing patients and HCs. Significant positive correlation was found between AD and age (Chao1 p.adj = .0004, Shannon p.adj = .0004, Simpson p.adj = .0028). BD depicted a different bacterial profile in the epilepsy groups compared to HCs (MS vs. HC: Bray-Curtis F = 1.783, p = .001; Jaccard F = 1.24, p = .001; MR vs. HC: Bray-Curtis F = 2.24, p = .001; Jaccard F = 1.364, p = .001). At the genus level, the epilepsy groups were characterized by a significant increase in Hungatella (MS vs. HC: +4.95 log2 change; MR vs. HC: +6.72 log2 change); the [Eubacterium] siraeum group changed between the MR and MS subgroups.

SIGNIFICANCE: Epileptic patients display unique gut metagenomic signatures compared to HCs. Moreover, a different ratio of the butyrate-producing [Eubacterium] siraeum group suggests dissimilarities between patients based on the response to antiseizure medications.},
}

Humans
*Gastrointestinal Microbiome/physiology
Male
Female
Child
*Drug Resistant Epilepsy/microbiology/drug therapy
Child, Preschool
Adolescent
Anticonvulsants/therapeutic use
Feces/microbiology
RNA, Ribosomal, 16S/genetics
Cohort Studies

@article {pmid40707722,
year = {2025},
author = {Mangnier, L and Bodein, A and Mariaz, M and Mathieu, A and Scott-Boyer, MP and Vashist, N and Bramble, MS and Droit, A},
title = {A systematic benchmark of integrative strategies for microbiome-metabolome data.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1100},
pmid = {40707722},
issn = {2399-3642},
mesh = {Humans ; *Metabolomics/methods ; *Metabolome ; *Gastrointestinal Microbiome ; Benchmarking ; *Metagenomics/methods ; *Microbiota ; Computational Biology/methods ; },
abstract = {The rapid advancement of high-throughput sequencing technologies has enabled the integration of various omic layers into computational frameworks. Among these, metagenomics and metabolomics are increasingly studied for their roles in complex diseases. However, no standard currently exists for jointly integrating microbiome and metabolome datasets within statistical models. We benchmarked nineteen integrative methods to disentangle the relationships between microorganisms and metabolites. These methods address key research goals, including global associations, data summarization, individual associations, and feature selection. Through realistic simulations, we identified the best-performing methods and validated them on real gut microbiome datasets, revealing complementary biological processes across the two omic layers. Practical guidelines are provided for specific scientific questions and data types. This work establishes a foundation for research standards in metagenomics-metabolomics integration and supports future methodological developments, while also providing guidance for designing optimal analytical strategies tailored to specific integration questions.},
}

Humans
*Metabolomics/methods
*Metabolome
*Gastrointestinal Microbiome
Benchmarking
*Metagenomics/methods
*Microbiota
Computational Biology/methods

@article {pmid40707492,
year = {2025},
author = {Villette, R and Novikova, PV and Laczny, CC and Mollenhauer, B and May, P and Wilmes, P},
title = {Human gut microbiome gene co-expression network reveals a loss in taxonomic and functional diversity in Parkinson's disease.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {142},
pmid = {40707492},
issn = {2055-5008},
support = {863664//HORIZON EUROPE European Research Council/ ; 863664//HORIZON EUROPE European Research Council/ ; CORE/16/BM/11333923//Fonds National de la Recherche Luxembourg/ ; CORE/16/BM/11333923//Fonds National de la Recherche Luxembourg/ ; },
mesh = {*Parkinson Disease/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Gene Regulatory Networks ; Metagenomics ; Gene Expression Profiling ; Male ; Female ; Aged ; Middle Aged ; },
abstract = {Gut microbiome alterations are linked to various diseases, including neurodegeneration, but their ecological and functional impacts remain unclear. Using integrated multi-omics (metagenomics and metatranscriptomics), we analyse microbiome gene co-expression networks in Parkinson's disease (PD) and healthy controls (HC). We observe a significant depletion of hub genes in PD, including genes involved in secondary bile acid biosynthesis, bacterial microcompartments (BMCs), polysaccharides transport and flagellar assembly (FA). Blautia, Roseburia, Faecalibacterium and Anaerobutyricum genera are the main contributors to these functions, showing significantly lower expression in PD. Additionally, we identify a strong correlation between BMC and FA expression, and an apparent dysregulation in cross-feeding between commensals in PD. Finally, PD also exhibits reduced gene expression diversity compared to HC, whereby higher gene expression correlates with greater diversity. We identify disruptions in gut metabolic functions, at both taxonomic and functional level, and microbiome-wide ecological features, highlighting targets for future gut microbiome restoration efforts.},
}

*Parkinson Disease/microbiology
*Gastrointestinal Microbiome/genetics
Humans
*Bacteria/classification/genetics/isolation & purification/metabolism
*Gene Regulatory Networks
Metagenomics
Gene Expression Profiling
Male
Female
Aged
Middle Aged

@article {pmid40707215,
year = {2025},
author = {Li-Hau, F and Nakagawa, M and Kakegawa, T and Ward, LM and Ueno, Y and McGlynn, SE},
title = {Metabolic Potential and Microbial Diversity of Late Archean to Early Proterozoic Ocean Analog Hot Springs of Japan.},
journal = {Microbes and environments},
volume = {40},
number = {3},
pages = {},
doi = {10.1264/jsme2.ME24067},
pmid = {40707215},
issn = {1347-4405},
mesh = {*Hot Springs/microbiology/chemistry ; Japan ; *Bacteria/classification/metabolism/genetics/isolation & purification ; *Archaea/classification/metabolism/genetics/isolation & purification ; Oxidation-Reduction ; Phylogeny ; Nitrogen Fixation ; Oceans and Seas ; Iron/metabolism ; *Biodiversity ; Carbon Cycle ; RNA, Ribosomal, 16S/genetics ; Nitrogen Cycle ; Hydrogen/metabolism ; },
abstract = {Circumneutral iron-rich hot springs may represent analogues of Neoarchean to Paleoproterozoic oceans of early Earth, potentially providing windows into ancient microbial ecology. Here we sampled five Japanese hot springs to gain insights into functional processes and taxonomic diversity in these analog environments. Amplicon and metagenomic sequencing confirm a hypothesis where taxonomy is distinct between sites and linked to the geochemical setting. Metabolic functions shared among the springs include carbon fixation via the reductive pentose phosphate cycle, nitrogen fixation, and dissimilatory iron oxidation/reduction. Among the sites, Kowakubi was unique in that it was dominated by Hydrogenophilaceae, a group known for performing hydrogen oxidation, motivating a hypothesis that H2 as an electron donor may shape community composition even in the presence of abundant ferrous iron. Evidence for nitrogen cycling across the springs included N2 fixation, dissimilatory nitrate reduction to ammonia (DNRA), and denitrification. The low-salinity springs Furutobe and OHK lacked evidence for ammonium oxidation by ammonia monooxygenase, but evidence for complete nitrification existed at Kowakubi, Jinata, and Tsubakiyama. In most sites, the microaerophilic iron-oxidizing bacteria from the Zetaproteobacteria or Gammaproteobacteria classes had higher relative abundances than Cyanobacteria. Microaerophilic iron oxidizers may outcompete abiotic Fe oxidation, while being fueled by oxy-phototrophic Cyanobacteria. Our data provide a foundation for considering which factors may have controlled productivity and elemental cycling as Earth's oceans became oxygenated at the onset of the Great Oxidation Event.},
}

*Hot Springs/microbiology/chemistry
Japan
*Bacteria/classification/metabolism/genetics/isolation & purification
*Archaea/classification/metabolism/genetics/isolation & purification
Oxidation-Reduction
Phylogeny
Nitrogen Fixation
Oceans and Seas
Iron/metabolism
*Biodiversity
Carbon Cycle
RNA, Ribosomal, 16S/genetics
Nitrogen Cycle
Hydrogen/metabolism

@article {pmid40703671,
year = {2025},
author = {Wang, Y and Lu, J and Dai, W and Yang, S},
title = {Jian-Pi-Yi-Shen formula improves kidney function by regulating gut microbiome in rats with chronic kidney disease.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1526863},
pmid = {40703671},
issn = {2235-2988},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Renal Insufficiency, Chronic/drug therapy/microbiology ; *Drugs, Chinese Herbal/pharmacology/administration & dosage ; Rats ; *Kidney/drug effects/physiopathology ; Disease Models, Animal ; Feces/microbiology ; Male ; Creatinine/blood ; Rats, Sprague-Dawley ; Metagenomics ; Medicine, Chinese Traditional ; },
abstract = {INTRODUCTION: Recent studies have underscored the role of interactions between Traditional Chinese Medicine (TCM) and the gut microbiome (GM) in mediating therapeutic effects. Jian-Pi-Yi-Shen Formula (JPYSF) has shown efficacy in ameliorating chronic kidney disease (CKD) symptoms, but its mechanisms via GM modulation remain unclear.

METHODS: In this study, 8-week-old rats were assigned to three groups after a two-week acclimation: C (normal diet for six weeks), M (adenine diet for four weeks then normal diet for two weeks), and T (same as M, with JPYSF administered during the final three weeks). Fecal samples were collected at three timepoints (T1: post-acclimation; T2: after three weeks on respective diets; T3: after three weeks of JPYSF treatment) for metagenomic sequencing. Serum creatinine (SCR) was measured at T2 and T3.

RESULTS: At T2, adenine-fed rats showed elevated SCR (C: 28.4 ± 1.5 µmol/L; M: 189.6 ± 25.8µmol/L; T: 186.4 ± 32.5µmol/L; p < 0.001). By T3, SCR decreased more in T (86.0 ± 14.9µmol/L) than in M (119.6 ± 16.3µmol/L; p = 0.012), with C remaining stable (30.8 ± 4.4µmol/L). Adenine feeding induced significant GM shifts, evidenced by increased Aitchison distance (p < 0.01) and altered co-abundance interaction groups (CIGs): CIG3, 6, 9, 10 increased; CIG1, 2, 4, 12 decreased (all p < 0.05). After JPYSF treatment, only CIG4 significantly rebounded (T3 vs. M, p = 0.0079), and T3-T1 dissimilarity was lower in T than M (p < 0.05). SCR levels were significantly lower in T than M after returning to a normal diet, suggesting a renoprotective effect of JPYSF. Co-occurrence analysis linked SCR positively with toxin-associated CIGs (CIG3, 6, 7, 9, 10) and pathways (purine metabolism, toluene degradation), and negatively with CIG4.

DISCUSSION: These results demonstrate that JPYSF lowers SCR and selectively modulates GM modules, particularly CIG4, which inversely correlates with uremic toxin-producing pathways, suggesting improved renal function and specific gut microbiota modulation in CKD rats.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Renal Insufficiency, Chronic/drug therapy/microbiology
*Drugs, Chinese Herbal/pharmacology/administration & dosage
Rats
*Kidney/drug effects/physiopathology
Disease Models, Animal
Feces/microbiology
Male
Creatinine/blood
Rats, Sprague-Dawley
Metagenomics
Medicine, Chinese Traditional

@article {pmid40702703,
year = {2025},
author = {Liu, X and Kong, J and Shan, Y and Yang, Z and Miao, J and Pan, Y and Luo, T and Shi, Z and Wang, Y and Gou, Q and Yang, C and Li, H and Li, C and Li, S and Zhang, X and Sun, Y and Holmes, EC and Guo, D and Shi, M},
title = {SegFinder: an automated tool for identifying complete RNA virus genome segments through co-occurrence in multiple sequenced samples.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {4},
pages = {},
doi = {10.1093/bib/bbaf358},
pmid = {40702703},
issn = {1477-4054},
support = {82341118//National Natural Science Foundation of China/ ; KQTD20200820145822023//Shenzhen Science and Technology Program/ ; MRP/071/20X//Hong Kong Innovation and Technology Fund/ ; GZNL2023A01001//Major Project of Guangzhou National Laboratory/ ; GZNL2023A01008//Major Project of Guangzhou National Laboratory/ ; 2019ZT08Y464//Guangdong Province 'Pearl River Talent Plan' Innovation, Entrepreneurship Team Project/ ; ZDSYS20220606100803007//Fund of Shenzhen Key Laboratory/ ; GNT2017197//NHMRC Investigator Award/ ; //Innovation and Technology Commission, Hong Kong Special Administrative Region, China/ ; },
mesh = {*Genome, Viral ; *RNA Viruses/genetics ; Animals ; *Computational Biology/methods ; Metagenomics/methods ; *Software ; RNA, Viral/genetics ; },
abstract = {Metagenomic sequencing has expanded the ribonucleic acid (RNA) virosphere, but many identified viral genomes remain incomplete, especially for segmented viruses. Traditional methods relying on sequence homology struggle to identify highly divergent segments and group them confidently within a single virus species. To address this, we developed a new bioinformatic tool-SegFinder-that identifies virus genome segments based on their common co-occurrence at similar abundance within segmented viruses. SegFinder successfully re-discovered all segments from a test data set of individual mosquito transcriptomes, which was also used to establish parameter thresholds for reliable segment identification. Using these optimal parameters, we applied SegFinder to 858 libraries from eight metagenomic sequencing projects, including vertebrates, invertebrates, plants, and environmental samples. Excluding the RdRP segment, we identified 106 unique viral genome segments from these samples. Among them, 53 were novel, including 30 segments that showed no recognizable sequence homology to any known viruses. However, the viral origin of these highly divergent segment was supported by the presence of conserved terminal sequences. SegFinder identifies segmented genome structures in viruses previously considered to be predominantly unsegmented, and in doing so expanded the number of known families and orders of segmented RNA viruses, making it a valuable tool in an era of large-scale parallel sequencing.},
}

*Genome, Viral
*RNA Viruses/genetics
Animals
*Computational Biology/methods
Metagenomics/methods
*Software
RNA, Viral/genetics

@article {pmid40697984,
year = {2025},
author = {Hebbar, P and Han, OB and Yan, NX and Kay, D and Chu, KY and Woon, JS and Lun, PK and Kabekkodu, SP and Prasad, ASB and Prakash, B and Nograles, N and Kanakal, MM and Goodson, M and Nagaraja, S and Mascarenhas, R},
title = {Characterization of microbiome diversity unveils substantial microbial variation in mangrove soil sediments from coastal regions of Malaysia.},
journal = {Access microbiology},
volume = {7},
number = {6},
pages = {},
pmid = {40697984},
issn = {2516-8290},
abstract = {The mangrove ecosystems are of great ecological importance found in tropical and subtropical coasts, including Malaysia. The microbial communities in the mangrove sediments play an indispensable role in maintaining homeostasis and supporting biodiversity. However, mangroves are facing various threats due to increasing anthropogenic activities. Thus, it is important to monitor the microbial community to improve our understanding of anthropogenic pressure on reshaping these ecosystems. This study examines the microbial community diversity in mangrove sediments of southern peninsular Malaysia. High-throughput MinION sequencing of the 16S rRNA gene was performed to compare the soil microbiome diversity in 35 samples from 8 different mangroves representing Sungai Sedili Kecil and Sungai Sedili Besar that flow into the South China Sea; Sungai Pulai, Sungai Melayu, Sungai Danga, Sungai Skudai and Sungai Johor that join the Straits of Johor; and Pulau Kukup from the Straits of Malacca. The metagenomic classification performed with 16S rRNA showed 2,573 taxa comprising 32 phyla. Total abundance analysis showed Pseudomonadota (67-69%), Bacteroidota (6-8%), Bacillota (5-8%), Campylobacterota (4-5%), Acidobacteriota (3-4%), Planctomycetota (2-4%) and Actinomycetota (1-2%) as the relatively common phyla. Alpha diversity indices revealed significantly higher richness in samples from mangroves of the South China Sea. Further, the 'Shannon' index showed a significant difference in diversity between Sungai Melayu and Sungai Pulai. Higher abundance of Burkholderiaceae, Bacillaceae and Enterobacteriaceae suggests a difference in the microbial community structure. This study stands as the first comprehensive analysis of microbial communities for future monitoring and conservation in these mangroves.},
}

@article {pmid40570415,
year = {2025},
author = {Yin, Z and Cao, K and Duan, N and Zhang, Z},
title = {Microbial community dynamics and functional potential during the natural fermentation of rose: A metagenomic and volatile compound analysis.},
journal = {Enzyme and microbial technology},
volume = {190},
number = {},
pages = {110703},
doi = {10.1016/j.enzmictec.2025.110703},
pmid = {40570415},
issn = {1879-0909},
mesh = {Fermentation ; *Volatile Organic Compounds/analysis/metabolism ; Metagenomics ; *Bacteria/genetics/classification/metabolism ; *Microbiota ; Metagenome ; *Microbial Consortia/genetics ; Butylene Glycols/metabolism ; },
abstract = {This study investigates the dynamics of microbial communities and their functional characteristics during the natural fermentation of roses. Utilizing metagenomic sequencing and volatile compound analysis, the research elucidates the succession of microbial communities and their relationship with the flavor compound production. The findings indicate that Klebsiella and Pichia are predominant in the early stages of fermentation, while Acetobacter and Cyberlindnera become more abundant in the middle and later stages. The glycosyltransferase (GT) family is identified as the primary carbohydrate-active enzyme (CAZy) family involved in fermentation, with GT1 and GT2 exhibiting a higher gene abundance. Functional genes are predominantly associated with the carbohydrate and amino acid metabolism. Analysis of volatile compounds reveals that substances such as phenethyl acetate and (S,S)-2,3-Butanediol are closely related to the structure of the microbial community. These findings contribute to a deeper understanding of the mechanisms underlying rose fermentation and offer a theoretical foundation for technological advancements in the rose product industry.},
}

Fermentation
*Volatile Organic Compounds/analysis/metabolism
Metagenomics
*Bacteria/genetics/classification/metabolism
*Microbiota
Metagenome
*Microbial Consortia/genetics
Butylene Glycols/metabolism

@article {pmid40568985,
year = {2025},
author = {Zhao, J and Brandt, G and Gronniger, JL and Wang, Z and Li, J and Hunt, DE and Rodriguez-R, LM and Hatt, JK and Konstantinidis, KT},
title = {Quantifying the contribution of the rare biosphere to natural disturbances.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf129},
pmid = {40568985},
issn = {1751-7370},
support = {OCE 1416673 and DEB 1831582//US National Science Foundation/ ; ICER 2033934, DEB 2224819//US National Science Foundation/ ; },
mesh = {Metagenome ; *Ecosystem ; *Microbiota ; },
abstract = {Understanding how populations respond to disturbances represents a major goal for microbial ecology. While several hypotheses have been advanced to explain microbial community compositional changes in response to disturbance, appropriate data to test these hypotheses is scarce, due to the challenges in delineating rare vs. abundant taxa and generalists vs. specialists, a prerequisite for testing the theories. Here, we operationally define these two key concepts by employing the patterns of coverage of a (target) genome by a metagenome to identify rare populations, and by borrowing the proportional similarity index from macroecology to identify generalists. We applied these concepts to time-series (field) metagenomes from the Piver's Island Coastal Observatory to establish that coastal microbial communities are resilient to major perturbations such as tropical cyclones and (uncommon) cold or warm temperature events, in part due to the response of rare populations. Therefore, these results provide support for the insurance hypothesis [i.e. the rare biosphere has the buffering capacity to mitigate the effects of disturbance]. Additionally, generalists appear to contribute proportionally more than specialists to community adaptation to perturbations like warming, supporting the disturbance-specialization hypothesis [i.e. disturbance favors generalists]. Several of these findings were also observed in replicated laboratory mesocosms that aimed to simulate disturbances such as a rain-driven washout of microbial cells and a labile organic matter release from a phytoplankton bloom. Taken together, our results advance understanding of the mechanisms governing microbial population dynamics under changing environmental conditions and have implications for ecosystem modeling.},
}

Metagenome
*Ecosystem
*Microbiota

@article {pmid40223739,
year = {2025},
author = {El Mouzan, M and Savidge, TC and Al Sarkhy, A and Badu, S and Alsaleem, B and Al Mofarreh, M and Almasood, A and Assiri, A},
title = {Gut virome profile in new onset treatment naïve Saudi children with ulcerative colitis.},
journal = {Saudi journal of gastroenterology : official journal of the Saudi Gastroenterology Association},
volume = {31},
number = {4},
pages = {212-218},
doi = {10.4103/sjg.sjg_24_25},
pmid = {40223739},
issn = {1998-4049},
mesh = {Humans ; *Colitis, Ulcerative/virology/microbiology/epidemiology ; Saudi Arabia/epidemiology ; Male ; Female ; *Gastrointestinal Microbiome/genetics ; Child ; *Virome/genetics ; Feces/virology/microbiology ; Adolescent ; Case-Control Studies ; *Bacteriophages/genetics/isolation & purification ; Metagenomics ; },
abstract = {BACKGROUND: Gut microbiome imbalance is well established in ulcerative colitis (UC) in Western populations. Significantly less is known about the gut virome and whether geography impacts the UC-associated microbiome. The aim of this study was to characterize gut bacteriophage changes, as well as to identify phage-bacterial associations that can serve as potential biomarkers of UC.

METHODS: Twenty children with UC and 20 healthy controls were enrolled in the study. Inclusion criteria included newly diagnosed treatment-naïve children with UC with no antibiotic exposure for at least six months prior to sample collection. Deoxyribonucleic acid (DNA) was extracted from stool and rectal biopsies and was processed for shotgun metagenomic sequencing. Bioinformatics and statistical analyses were performed to assess phage diversity and their associations with gut bacteria. Candidate biomarkers were identified using the random forest classifier.

RESULTS: In fecal samples, bacteriophage diversity was not significantly altered, but 72 species were significantly altered in UC, five of which (Salmonella_phage_SEN4 , uncultured_crAssphage, Staphylococcus_phage_SPbeta-like , Streptococcus_phage_YMC-2011 and Siphoviridae_u_s) were identified as candidate biomarker signatures.

CONCLUSIONS: We found a significantly altered bacteriophage signature in children with new onset, treatment naïve UC in Saudi children, a Middle Eastern population. These changes differed from previously reported Western UC cases, indicating that demographic bias needs to be considered when developing microbiota-based diagnostics and therapeutic applications for non-Western populations.},
}

Humans
*Colitis, Ulcerative/virology/microbiology/epidemiology
Saudi Arabia/epidemiology
Male
Female
*Gastrointestinal Microbiome/genetics
Child
*Virome/genetics
Feces/virology/microbiology
Adolescent
Case-Control Studies
*Bacteriophages/genetics/isolation & purification
Metagenomics

@article {pmid40696437,
year = {2025},
author = {Ashton, PM and Mageiros, L and Meiring, JE and Chunga-Chirambo, A and Khanam, F and Dongol, S and Banda, H and Karkey, A and Preciado-Llanes, L and Thomaides-Brears, H and Gibani, M and Rajib, NH and Rahman, N and Biswas, PK and Bhuiyan, MAI and Kay, S and Auger, K and Seret, O and Thomson, NR and Pollard, AJ and Baker, S and Basnyat, B and Clemens, JD and Dolecek, C and Dunstan, SJ and Dougan, G and Heyderman, RS and Pitzer, VE and Qadri, F and Gordon, MA and Holt, KE and Darton, TC and , },
title = {Interplay between the gut microbiome and typhoid fever: insights from endemic countries and a controlled human infection model.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {168},
pmid = {40696437},
issn = {2049-2618},
mesh = {Humans ; *Typhoid Fever/microbiology/epidemiology ; *Gastrointestinal Microbiome ; *Salmonella typhi/pathogenicity ; Prospective Studies ; Male ; Female ; Malawi/epidemiology ; Adult ; Bangladesh/epidemiology ; Nepal/epidemiology ; Adolescent ; Child ; Feces/microbiology ; Young Adult ; Endemic Diseases ; Fatty Acids, Volatile/metabolism ; Middle Aged ; Child, Preschool ; },
abstract = {BACKGROUND: Typhoid fever is a systemic infection caused by Salmonella enterica serovar Typhi (S. Typhi) invasion from the gut lumen. Transmission between people occurs through ingestion of contaminated food and water, particularly in settings with poor water and sanitation infrastructure, resulting in over 10 million illnesses annually. As the pathogen invades via the gastrointestinal tract, it is plausible that the gut microbiome may influence the outcome of S. Typhi exposure. There is some evidence that bacteria producing short-chain fatty acids (SCFAs) may create an environment unfavourable to invasive Salmonella, but data from humans is limited.

METHODS: To investigate the association between the gut microbiome and typhoid fever, we analysed samples collected from three all-age cohorts enrolled in a prospective surveillance study conducted across three settings where typhoid fever is endemic (Dhaka, Bangladesh; Blantyre, Malawi; and Kathmandu, Nepal). Cohorts consisted of acute typhoid fever patients (n = 92), asymptomatic household contacts of typhoid fever patients (representing individuals who were likely exposed to S. Typhi but did not develop the disease, n = 97) and asymptomatic serosurvey participants with high Vi antibody titres (representing individuals who were exposed to S. Typhi and may be carriers, n = 69). The stool microbiomes of each cohort were characterised using shotgun metagenomics, and bacterial diversity, composition and function were compared.

RESULTS: We identified 4 bacterial species that were significantly lower in abundance in typhoid fever patients compared with household contacts (i.e. probably exposed), in two of the three participant populations (Bangladesh and Malawi). These bacteria may represent taxa that provide protection against the development of clinical infection upon exposure to S. Typhi and include the inflammation-associated species Prevotella copri clade A and Haemophilus parainfluenzae. Our functional analysis identified 28 specific metabolic gene clusters (MGCs) negatively associated with typhoid fever in Bangladesh and Malawi, including seven MGCs involved in SCFA metabolism. The putative protection provided by microbiome SCFA metabolism was supported by data from a controlled human infection model conducted in a UK population, in which participants who did not develop typhoid fever following ingestion of S. Typhi had a higher abundance of a putative SCFA-metabolising MGC (q-value = 0.22).

CONCLUSIONS: This study identified the same protective associations between taxonomic and functional microbiota characteristics and non-susceptibility to typhoid fever across multiple human populations. Future research should explore the potential functional role of SCFAs and inflammation-associated bacteria in resistance to S. Typhi and other enteric infections. Video Abstract.},
}

Humans
*Typhoid Fever/microbiology/epidemiology
*Gastrointestinal Microbiome
*Salmonella typhi/pathogenicity
Prospective Studies
Male
Female
Malawi/epidemiology
Adult
Bangladesh/epidemiology
Nepal/epidemiology
Adolescent
Child
Feces/microbiology
Young Adult
Endemic Diseases
Fatty Acids, Volatile/metabolism
Middle Aged
Child, Preschool

@article {pmid40695901,
year = {2025},
author = {Awad, N and Larson, PJ and Sissoko, CA and Bond, LL and Dion, GR},
title = {Metagenomic whole genome shotgun analysis of the airway microbiome in laryngotracheal stenosis: a pilot study.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {26570},
pmid = {40695901},
issn = {2045-2322},
mesh = {Humans ; Pilot Projects ; *Microbiota/genetics ; *Laryngostenosis/microbiology ; *Tracheal Stenosis/microbiology ; Male ; Female ; Middle Aged ; *Metagenomics/methods ; Aged ; Metagenome ; Adult ; Tracheostomy ; Whole Genome Sequencing ; RNA, Ribosomal, 16S/genetics ; Shotgun Sequencing ; },
abstract = {The airway microbiome has been implicated in the pathogenesis of laryngotracheal stenosis (LTS), yet prior studies using 16 S rRNA sequencing have limited sub-genus level resolution. Metagenomic whole genome shotgun sequencing (mWGS) allows for strain-level taxonomic and functional genomic analysis, providing detailed insights into specific organisms and pathways. A pilot study was conducted to explore the advantages and challenges of mWGS in investigating the airway metagenome in LTS. mWGS was conducted on 12 intraoperative swab samples from 8 LTS patients, divided into tracheostomy-dependent (n = 3) and non-tracheostomy (n = 5) groups, and 4 controls. Patient comorbidities, antibiotic use, and medications were documented. Biobakery workflows were used for taxonomic and functional profiling. Species-specific reference databases were constructed for 6 abundant species for strain-level analyses. LTS samples had decreased taxonomic diversity and were dominated by species with previously described roles in other chronic inflammatory processes such as Staphylococcus aureus, Streptococcus parasanguinis, Streptococcus mitis, and Corynebacterium pseudogenitalium. LTS samples were enriched for pathways involved in fatty acid biosynthesis and formaldehyde metabolism. Our results identified tracheostomy as an important potential confounder in airway metagenomics but show mWGS techniques are promising in uncovering microbiota correlates in LTS that could reveal disease-specific biomarkers, comorbidity links, and therapeutic targets.},
}

Humans
Pilot Projects
*Microbiota/genetics
*Laryngostenosis/microbiology
*Tracheal Stenosis/microbiology
Male
Female
Middle Aged
*Metagenomics/methods
Aged
Metagenome
Adult
Tracheostomy
Whole Genome Sequencing
RNA, Ribosomal, 16S/genetics
Shotgun Sequencing

@article {pmid40692682,
year = {2025},
author = {Qin, X and Xi, L and Zhao, L and Han, J and Qu, H and Xu, Y and Weng, W},
title = {Exploring the distinctive characteristics of gut microbiota across different horse breeds and ages using metataxonomics.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1590839},
pmid = {40692682},
issn = {2235-2988},
mesh = {Animals ; Horses/microbiology ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Age Factors ; Metagenomics/methods ; DNA, Bacterial/genetics ; Biodiversity ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Gut microbiota exerts a pivotal function in host nutrient metabolism and maturation of the mucosal immunity. Analyzing the reciprocal interaction between horses and gut microbiota constitutes a crucial aspect of scientific feeding practices. This study aims to investigate the differences in gut microbiota among Hequ horses, Mongolian horses, and Thoroughbred horses, as well as between Thoroughbred horses at two age stages.

METHODS AND RESULTS: Paired-end sequencing with a read length of 2×250 bp targeting the V3-V4 region of the 16S rRNA gene in fecal samples was carried out. Subsequently, differences in the diversity, composition, and metabolic pathways of the gut microbiota among the groups were analyzed. The results showed that: (1) Horse breeds were associated with variations in the gut microbiota. Microbial diversity, the proportion of commensal bacteria from Bacillota and Bacteroidota, and bacterial communities involved in dietary fiber metabolisms were significantly higher in the gut of the Hequ horses than in the gut of the Mongolian and Thoroughbred horses. The highest Bacillota to Bacteroidota (B/B) ratio and enrichment of bacterial communities involved in the metabolism of bile acids, lipids, and amino acids in the gut of the Mongolian horses resulted in significantly higher lipid metabolism and amino acid metabolism than in the other two breeds. The bacterial communities enriched in the gut of Thoroughbred horses were primarily involved in carbohydrate metabolism, but the level of energy metabolism was significantly lower than in Hequ horses. (2) The results also showed an association between age and gut microbiota of Thoroughbred horses. The alpha diversity, B/B ratio, and 83.33% of metabolic pathways did not differ significantly between younger and older Thoroughbred horses. However, there were significant differences between the two age groups in beta diversity, composition of glycolytic bacteria, metabolism of cofactors and vitamins, and energy metabolism of gut microbiota.

CONCLUSIONS: Collectively, these results point to an association between the breed of horses or the age of Thoroughbred horses with variations in gut microbiota. The current findings will serve as a reference for improving feeding strategies for horses.},
}

Animals
Horses/microbiology
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
Feces/microbiology
*Bacteria/classification/genetics/isolation & purification/metabolism
Age Factors
Metagenomics/methods
DNA, Bacterial/genetics
Biodiversity
Sequence Analysis, DNA

@article {pmid40607849,
year = {2025},
author = {Zhang, H and Zhao, D and Wu, QL and Zeng, J},
title = {Environment selected microbial function rather than taxonomic species in a plateau saline-alkaline wetland.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {7},
pages = {e0220624},
doi = {10.1128/aem.02206-24},
pmid = {40607849},
issn = {1098-5336},
support = {U23A20153//National Natural Science Foundation of China/ ; BT2024012//Jiangsu Provincial Innovation Research Program on Carbon Peaking and Carbon Neutrality/ ; B240205024//Fundamental Research Funds for the Central Universities/ ; 2023YFF1304501//National Key R&D Program of China/ ; XDB0810000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; },
mesh = {*Wetlands ; *Soil Microbiology ; *Microbiota ; Salinity ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Methane/metabolism ; Nitrogen/metabolism ; Tibet ; Geologic Sediments/microbiology ; Metagenome ; Rhizosphere ; },
abstract = {UNLABELLED: Comprehending the microbial community in plateau saline-alkaline wetlands, an understudied and vulnerable ecosystem, is vital for predicting ecosystem functions within the context of global climate change. Despite the rapid shrinkage and potential drying up of some of these wetlands, our knowledge of the microbial community in this ecosystem remains fragmented. Here, we utilized metagenomic sequencing to investigate the distribution of methane, nitrogen, and sulfur cycling genes/pathways and formation mechanism of microbial communities across sediment, surface rhizosphere soils (Rsurface), subsurface rhizosphere soils (Rsubsurface), surface bulk soils (Bsurface), and subsurface bulk soils (Bsubsurface) in Cuochuolong Wetland, a typical saline-alkaline wetland located in the Tibetan Plateau. The results showed that sediment exhibited relatively higher functional potentials for methanogenesis but lower potentials for methane oxidation. Denitrification and dissimilatory sulfate reduction potentials increased with decreasing salinity across the five habitats, following the trend: sediment
IMPORTANCE: Understanding the formation mechanism of microbial communities is a central goal in ecology. However, our understanding of microbial community remains fragmented in plateau saline-alkaline wetlands, despite their unique status as a vulnerable ecosystem characterized by high altitude, low disturbance, high salinity, sensitivity to global climate change, and localized shrinkage in some areas. Furthermore, previous studies on community formation mechanism have predominantly focused on microbial taxonomic structure, neglecting their functional compositions. Beyond providing a comprehensive understanding of the distribution patterns of methane, nitrogen, and sulfur cycling microbial communities within plateau saline-alkaline wetland, this study offers a novel perspective on formation mechanism of microbial community by emphasizing the deterministic selection of extreme environment on microbial function. This study also expands our comprehension of the diversity of microbes containing the nod gene, which may substantially contribute to global methane and nitrogen budgets.},
}

*Wetlands
*Soil Microbiology
*Microbiota
Salinity
*Bacteria/classification/genetics/metabolism/isolation & purification
Methane/metabolism
Nitrogen/metabolism
Tibet
Geologic Sediments/microbiology
Metagenome
Rhizosphere

@article {pmid40607829,
year = {2025},
author = {Williams, A and Ravel, J and Armstrong, E and Huibner, S and Rutt, L and Kaul, R and Holm, JB},
title = {Temporal dynamics of the vaginal microbiome and host immune markers before, during, and after metronidazole treatment for bacterial vaginosis.},
journal = {mSystems},
volume = {10},
number = {7},
pages = {e0038025},
pmid = {40607829},
issn = {2379-5077},
support = {UH2AI083264//National Institute of Allergy and Infectious Diseases/ ; K01 AI163413/AI/NIAID NIH HHS/United States ; K01-AI163413//National Institute of Allergy and Infectious Diseases/ ; ID #884//University of Maryland Baltimore Institute for Clinical & Translational Research/ ; T32AI162579//National Institute of Allergy and Infectious Diseases/ ; },
mesh = {Humans ; Female ; *Vaginosis, Bacterial/drug therapy/microbiology/immunology ; *Metronidazole/therapeutic use/pharmacology ; *Vagina/microbiology/immunology/drug effects ; *Microbiota/drug effects ; Adult ; Biomarkers ; Young Adult ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {This study analyzed metagenomic and immune marker profiles of seven individuals before, during, and after a 7-day course of metronidazole treatment for bacterial vaginosis (BV). Treatment reduced BV-associated bacteria and immune marker levels, with distinct early (days 1-4) and late (days 5-7) phases. Post-treatment variability in microbial and immune marker profiles demonstrated a rapid resurgence of certain BV-associated bacteria, highlighting the need for additional strategies like probiotics to maintain a healthy vaginal microbiome. The study found significant host and microbial influences on immune response variance, with IP-10 and sEcad highly correlated with the vaginal microbiome. The findings identify the optimal timing for administering live biotherapeutics to restore D-lactic acid-producing Lactobacillus species dominance and underscore the complexity of BV infection and treatment response among different people.IMPORTANCEBacterial vaginosis (BV), a common condition associated with an increased risk of preterm birth and sexually transmitted infections, among others, is characterized by a dysbiotic vaginal microbiome associated with the predominance of a diverse assortment of anaerobic bacterial species. Metronidazole is the first-line treatment recommended by the CDC for BV when patients report symptoms. Despite treatment, BV recurrence is common. There is limited data regarding the effects of oral metronidazole on the vaginal microbiome starting at the initiation of treatment, as most studies have compared measurements taken before and after treatment completion. This study utilized metagenomic sequencing, pan-bacterial qPCR, and immune marker measurements to analyze the longitudinal dynamics of the vaginal microbiome and host immune response before, during, and after metronidazole treatment.},
}

Humans
Female
*Vaginosis, Bacterial/drug therapy/microbiology/immunology
*Metronidazole/therapeutic use/pharmacology
*Vagina/microbiology/immunology/drug effects
*Microbiota/drug effects
Adult
Biomarkers
Young Adult
Anti-Bacterial Agents/therapeutic use

@article {pmid40604156,
year = {2025},
author = {Kim, H and Nelson, P and Nzabarushimana, E and Shen, J and Jensen, J and Bhosle, A and Li, C and Lee, N and Everett, C and Berdy, B and Frongillo, G and Livny, J and Hu, FB and Simon, TG and McIver, L and Franzosa, EA and Chan, AT and Hayete, B and Thompson, KN and Huttenhower, C and Nguyen, LH},
title = {Multi-omic analysis reveals transkingdom gut dysbiosis in metabolic dysfunction-associated steatotic liver disease.},
journal = {Nature metabolism},
volume = {7},
number = {7},
pages = {1476-1492},
pmid = {40604156},
issn = {2522-5812},
support = {K23DK125838//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; T32CA009001//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R35CA253185//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R24DK110499//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; Research Scholars Award//American Gastroenterological Association (AGA)/ ; Career Development Award//Crohn's and Colitis Foundation (Crohn's & Colitis Foundation)/ ; Research Professorship//American Cancer Society (American Cancer Society, Inc.)/ ; },
mesh = {Humans ; *Dysbiosis/microbiology/metabolism ; *Gastrointestinal Microbiome/genetics ; Female ; *Fatty Liver/microbiology/metabolism ; Metabolome ; Middle Aged ; Metagenome ; Adult ; Metagenomics ; Feces/microbiology ; Multiomics ; },
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is a common condition linked to obesity and the metabolic syndrome, yet its transkingdom connections have been under-investigated. We performed high-resolution multi-omic profiling-including stool metagenomes, metatranscriptomes and metabolomes-in 211 MASLD cases and 502 controls from a cohort of female nurses. Here we show that MASLD is associated with shifts in 66 gut bacterial species, including widespread enrichment of oral-typical microbes, and transkingdom dysbiosis involving not only bacterial but also viral taxa. Streptococcus spp. are more abundant in non-lean versus lean MASLD, the latter being a paradoxical subtype of a disease typically associated with increased adiposity. These microbial changes correspond with shifts in transcripts and metabolites, including increases in polyamines and acylcarnitines and reductions in secondary bile acids. We highlight gut viral perturbations in MASLD, showing that expansions of bacteriophage targeting oral-typical bacteria correspond to expansions of their bacterial hosts in the gut. We provide a comprehensive resource for understanding MASLD and highlight transkingdom multi-omic microbial shifts as potential contributors to its aetiopathogenesis.},
}

Humans
*Dysbiosis/microbiology/metabolism
*Gastrointestinal Microbiome/genetics
Female
*Fatty Liver/microbiology/metabolism
Metabolome
Middle Aged
Metagenome
Adult
Metagenomics
Feces/microbiology
Multiomics

@article {pmid40600712,
year = {2025},
author = {Comeault, AA and Orta, AH and Fidler, DB and Nunn, T and Ellison, AR and Anspach, TA and Matute, DR},
title = {Phylogenetic and functional diversity among Drosophila-associated metagenome-assembled genomes.},
journal = {mSystems},
volume = {10},
number = {7},
pages = {e0002725},
pmid = {40600712},
issn = {2379-5077},
support = {RGS\R1\221323//Royal Society/ ; R35GM148244/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Phylogeny ; *Metagenome/genetics ; *Drosophila/microbiology/genetics ; *Bacteria/genetics/classification ; *Genome, Bacterial ; Gastrointestinal Microbiome/genetics ; Microbiota ; },
abstract = {Host-associated microbial communities can mediate interactions between their hosts and biotic and abiotic environments. While much work has been done to document how microbiomes vary across species and environments, much less is known about the functional consequences of this variation. Here, we test for functional variation among drosophilid-associated bacteria by conducting Oxford Nanopore long-read sequencing and generating metagenome-assembled genomes (MAGs) from communities associated with six species of drosophilid flies collected from "anthropogenic" environments in North America, Europe, and Africa. Using phylogenetic analyses, we find that drosophilid flies harbor a diverse microbiome that includes core members closely related to the genera Gilliamella, Orbus, Entomomonas, Dysgonomonas, and others. Comparisons with publicly available bacterial genomes show that many of these genera are associated with phylogenetically diverse insect gut microbiomes. Using functional annotations and predicted secondary metabolite biosynthetic gene clusters, we show that MAGs belonging to different bacterial orders and genera vary in gene content and predicted functions, including metabolic capacity and how they respond to environmental stressors. Our results provide evidence that wild drosophilid flies harbor phylogenetically and functionally diverse microbial communities. These findings highlight a need to quantify the abundance and function of insect-associated bacteria from the genera Gilliamella, Orbus, Entomomonas, and others on the performance of their insect hosts across diverse environments.IMPORTANCEWhile much attention has been given to catalogue the taxonomic diversity intrinsic to host-associated microbiomes, much less is known about the functional consequences of this variation, especially in wild, non-model host species. In this study, we use long-read sequencing to generate and analyze 103 high-quality metagenome-assembled genomes from host-associated bacterial communities from six species of wild fruit fly (Drosophila). We find that the genomes of drosophilid-associated bacteria possess diverse metabolic pathways and biosynthetic gene clusters that are predicted to generate metabolites involved in nutrition and disease resistance, among other functions. Using functional gene predictions, we show that different bacterial lineages that comprise the insect microbiome differ in predicted functional capacities. Our findings highlight the functional variation intrinsic to microbial communities of wild insects and provide a step towards disentangling the ecological and evolutionary processes driving host-microbe symbioses.},
}

Animals
*Phylogeny
*Metagenome/genetics
*Drosophila/microbiology/genetics
*Bacteria/genetics/classification
*Genome, Bacterial
Gastrointestinal Microbiome/genetics
Microbiota

@article {pmid40586597,
year = {2025},
author = {Khatib, L and Song, SJ and Dilmore, AH and Sanders, JG and Brennan, C and Hernandez, AR and Myers, T and Oles, R and Farmer, S and Cowart, C and Birmingham, A and Diaz, EA and Nizet, O and Gilbert, K and Litwin, N and Das, P and Nowinski, B and Bryant, M and Tribelhorn, C and Sanders-Bodai, K and Chaumont, S and Knol, J and Roeselers, G and Laiola, M and Shetty, SA and Veiga, P and Tap, J and Derrien, M and Koutnikova, H and Cotillard, A and Lay, C and Tovar, AR and Torres, N and Arteaga, L and González, A and McDonald, D and Bartko, A and Knight, R},
title = {A three-country analysis of the gut microbiome indicates taxon associations with diet vary by taxon resolution and population.},
journal = {mSystems},
volume = {10},
number = {7},
pages = {e0054425},
pmid = {40586597},
issn = {2379-5077},
support = {//Danone Nutricia Research/ ; //Center for Microbiome Innovation/ ; //Microsetta Initative/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Diet ; Feces/microbiology ; Metagenomics/methods ; Male ; Female ; Adult ; Metagenome ; Prevotella/genetics/classification/isolation & purification ; Middle Aged ; Faecalibacterium/genetics/classification/isolation & purification ; },
abstract = {UNLABELLED: Emerging research suggests that diet plays a vital role in shaping the composition and function of the gut microbiota. Although substantial efforts have been made to identify general patterns linking diet to the gut microbiome, much of this research has been concentrated on a small number of countries. Additionally, both diet and the gut microbiome have highly complex and individualized configurations, and there is growing evidence that tailoring diets to individual gut microbiota profiles may optimize the path toward improving or maintaining health and preventing disease. Using fecal metagenomic data from 1,177 individuals across three countries, we examine the relationship between diet and bacterial genera, focusing on Prevotella and Faecalibacterium, which have gained significant attention for their potential roles in human health and strong associations with dietary patterns. We find that these two genera in particular show significant associations with many aspects of diet but these associations vary in scale and direction, depending on the level of metagenomic resolution (i.e., genus level by reads and strain level by metagenome-assembled genomes) and the contextual population. These results highlight the growing importance of building metagenomic data sets that are standardized, comprehensive, and representative of diverse populations to increase our ability to tease apart the complex relationship between diet and the microbiome.

IMPORTANCE: An analysis of fecal microbiome data from individuals in the United States, United Kingdom, and Mexico shows that associations with dietary components vary both by country and by level of resolution (i.e., genus and strain). Our work sheds light on why there may be conflicting reports regarding microbial associations with diet, disease, and health.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Diet
Feces/microbiology
Metagenomics/methods
Male
Female
Adult
Metagenome
Prevotella/genetics/classification/isolation & purification
Middle Aged
Faecalibacterium/genetics/classification/isolation & purification

@article {pmid40586419,
year = {2025},
author = {Dason, MS and Corà, D and Re, A},
title = {Sequence modeling tools to decode the biosynthetic diversity of the human microbiome.},
journal = {mSystems},
volume = {10},
number = {7},
pages = {e0033325},
pmid = {40586419},
issn = {2379-5077},
support = {P2022AFS8P//Next Generation EU - MUR/ ; },
mesh = {Humans ; *Microbiota/genetics ; *Biosynthetic Pathways/genetics ; Multigene Family ; *Computational Biology/methods ; Bacteria/genetics/metabolism ; },
abstract = {Understanding the biosynthetic potential of the human microbiome remains a significant challenge with far-reaching scientific and translational implications. Analyses of human-associated (meta)genomic sequencing data undeniably show that the biosynthetic diversity encoded in these genomes is largely underexplored. A crucial step in studying specialized metabolites involves the sequence-based identification of genes encoding biosynthetic pathways, typically organized into biosynthetic gene clusters (BGCs). In this review, we provide a concise and updated overview of the widening range of computational approaches that have effectively addressed the sequence-based identification of BGCs across both isolated genomes and complex microbial communities. These advancements are set to deepen our understanding of the biosynthetic potential and diversity of microorganisms residing in different human body sites.},
}

Humans
*Microbiota/genetics
*Biosynthetic Pathways/genetics
Multigene Family
*Computational Biology/methods
Bacteria/genetics/metabolism

@article {pmid40582607,
year = {2025},
author = {Páez-Triana, L and Luna, N and Cruz-Saavedra, L and Ramírez, AL and Medina, JE and Castañeda, S and Gómez, M and Garcia-Corredor, DJ and Medellín, MOP and Patiño, LH and Muñoz, M and Ramirez, JD},
title = {Characterizing the diversity of Rhipicephalus sanguineus sensu lato (s.l) virome in Colombia.},
journal = {Acta tropica},
volume = {268},
number = {},
pages = {107715},
doi = {10.1016/j.actatropica.2025.107715},
pmid = {40582607},
issn = {1873-6254},
mesh = {Animals ; Colombia ; *Rhipicephalus sanguineus/virology ; *Virome ; Phylogeny ; Dogs ; Genome, Viral ; *RNA Viruses/genetics/classification/isolation & purification ; Nanopore Sequencing ; Female ; },
abstract = {Ticks within the species complex Rhipicephalus sanguineus sensu lato are carriers for various pathogens worldwide. Among them are some RNA viruses, who have gained increased attention due to their potential for interaction between pathogenic and non-pathogenic organism. Our study aimed to investigate the RNA virus composition in R. sanguineus s.l. (also known as R. linnaei) ticks collected from the Santander and Casanare regions in eastern Colombia. We employed Oxford Nanopore sequencing technology coupled with viral enrichment procedures. Thirty-nine adult ticks, removed from dogs, were sequenced with Oxford Nanopore sequencing. These reads underwent two distinct analyses: one focused on sequencing reads utilizing Centrifuge/BLAST for direct assignment, and one involved assembly of viral metagenomic assembled genomes (vMAGs) using the Genome Detective Tool program. Our investigation showed the presence of six distinct viruses within the tick virome: Trinbago virus, Mivirus sp., Bole tick virus 4, Brown dog tick phlebovirus 2, Totiviridae sp., Ixodes scapularis totilike virus, and Brown dog tick phlebovirus 1. Notably, we successfully assembled the genomes for the latter two species, enabling phylogenetic and comparative analyses with genomes from various global regions. Only the category of sex yield significant differences in alpha diversity. We described viruses with potential pathogenicity but also with endosymbiotic potential. The latter group holds promise for developing biotechnological tools to aid future tick vector control strategies. Furthermore, our research offered valuable insights into the predominant viruses found in R. sanguineus s.l. ticks in two previously unexplored regions within Colombia.},
}

Animals
Colombia
*Rhipicephalus sanguineus/virology
*Virome
Phylogeny
Dogs
Genome, Viral
*RNA Viruses/genetics/classification/isolation & purification
Nanopore Sequencing
Female

@article {pmid40539782,
year = {2025},
author = {Qi, Y-H and Ye, Z-X and Feng, K-H and Ma, X-W and Zhang, C-X and Hu, M-H and Shi, M and Chen, J-P and Li, J-M},
title = {Diversity and evolutionary history of RNA viruses among different horseshoe crab species.},
journal = {Journal of virology},
volume = {99},
number = {7},
pages = {e0016425},
pmid = {40539782},
issn = {1098-5514},
support = {2022ZD03//Key Laboratory of Tropical Marine Ecosystem and Bioresource, Ministry of Natural Resources/ ; 2019B10004//Ningbo Science and Technology Innovation 2025 Major Project/ ; },
mesh = {Animals ; *Horseshoe Crabs/virology/classification ; *RNA Viruses/genetics/classification ; Phylogeny ; *Evolution, Molecular ; Genome, Viral ; Genetic Variation ; Virome ; },
abstract = {Horseshoe crabs (Xiphosura: Limulidae) are the sole surviving species of the class Merostomata, with only four extant species remaining today. Recent advances in metagenomic next-generation sequencing have unveiled a vast diversity of RNA viruses and non-retroviral endogenous RNA viral elements (nrEVEs) in invertebrates. This raises intriguing questions about the RNA virome and nrEVEs in horseshoe crabs as "living fossils," potentially offering insights into the evolutionary relationships between RNA viruses and these ancient organisms. In this study, 22 novel RNA viruses were identified across the four horseshoe crab species by screening 117 data sets, including picornaviruses, totiviruses, a flavivirus, a rhabdovirus, as well as a plant-associated tombusvirus and a fungi-associated narnavirus. Additionally, 20 nrEVEs were identified in the genomes of the four horseshoe crab species (hcEVEs), with most sharing homology with the viral family Chuviridae (N = 11), supporting the hypothesis that modern negative-sense RNA viruses may trace their origins to ancient oceanic chuviruses. A time-scaled phylogenetic tree based on hcEVEs suggests that at least two independent ancient chuvirus infections and genome integration events occurred in the common ancestor of horseshoe crab species. Interestingly, transcriptional analyses indicated that hcEVE-containing transcripts display typical exon-intron structures in the three Asian horseshoe crab species, suggesting that these hcEVEs may have been co-opted by horseshoe crabs during coevolution. These findings advance our understanding of the RNA viruses associated with horseshoe crabs and shed light on the potential role of RNA viruses in shaping the evolutionary history of this "living fossil" arthropod host.IMPORTANCERecent studies have discovered abundant RNA viruses in invertebrates, revealing that viral genomes may integrate into host genomes, creating a genetic record of past infections. In this study, we explored the evolutionary relationship between RNA viruses and the four extant horseshoe crab species-the last representatives of the class Merostomata, often termed "living fossils"-by analyzing viral sequences embedded in their genomes. The presence of chuvirus-like sequences in the genomes of these horseshoe crabs suggests that modern negative-sense RNA viruses may trace their origins back to ancient chuviruses from the ocean. Furthermore, we identified at least two independent ancient integrations of chuviruses in the evolutionary history of horseshoe crabs, with one orthologous gene containing a chuvirus-derived G protein gene/coding sequence potentially inherited from a common ancestor of the three Asian species before their divergence. Our findings contribute to a deeper understanding of the long-term coevolution between RNA viruses and their arthropod hosts.},
}

Animals
*Horseshoe Crabs/virology/classification
*RNA Viruses/genetics/classification
Phylogeny
*Evolution, Molecular
Genome, Viral
Genetic Variation
Virome

@article {pmid40530883,
year = {2025},
author = {Ganote, CL and Caesar, L and Rice, DW and Whitaker, RJ and Newton, ILG},
title = {Evolutionary trends in Bombella apis CRISPR-Cas systems.},
journal = {mSystems},
volume = {10},
number = {7},
pages = {e0016625},
pmid = {40530883},
issn = {2379-5077},
support = {2005306//National Science Foundation/ ; },
mesh = {*CRISPR-Cas Systems/genetics ; Animals ; Bees/microbiology/genetics ; *Evolution, Molecular ; Gastrointestinal Microbiome ; Phylogeny ; },
abstract = {UNLABELLED: Bacteria and archaea employ a rudimentary immune system, CRISPR-Cas, to protect against foreign genetic elements such as bacteriophage. CRISPR-Cas systems are found in Bombella apis. B. apis is an important honey bee symbiont, found primarily in larvae, queens, and hive compartments. B. apis is found in the worker bee gut but is not considered a core member of the bee microbiome and has therefore been understudied with regard to its importance in the honey bee colony. However, B. apis appears to play beneficial roles in the colony, by protecting developing brood from fungal pathogens and by bolstering their development under nutritional stress. Previously, we identified CRISPR-Cas systems as being acquired by B. apis in its transition to bee association, as they are absent in a sister clade. Here, we assess the variation and distribution of CRISPR-Cas types across B. apis strains. We found multiple CRISPR-Cas types, some of which have multiple arrays, within the same B. apis genomes and also in the honey bee queen gut metagenomes. We analyzed the spacers between strains to identify the history of mobile element interaction for each B. apis strain. Finally, we predict interactions between viral sequences and CRISPR systems from different honey bee microbiome members. Our analyses show that the B. apis CRISPR-Cas systems are dynamic; that microbes in the same niche have unique spacers, which supports the functionality of these CRISPR-Cas systems; and that acquisition of new spacers may be occurring in multiple locations in the genome, allowing for a flexible antiviral arsenal for the microbe.

IMPORTANCE: Honey bee worker gut microbes have been implicated in everything from protection from pathogens to breakdown of complex polysaccharides in the diet. However, there are multiple niches within a honey bee colony that host different groups of microbes, including the acetic acid bacterium Bombella apis. B. apis is found in the colony food stores, in association with brood, in worker hypopharyngeal glands, and in the queen's digestive tract. The roles that B. apis may serve in these environments are just beginning to be discovered and include the production of a potent antifungal that protects developing bees and supplementation of dietary lysine to young larvae, bolstering their nutrition. Niche specificity in B. apis may be affected by the pressures of bacteriophage and other mobile elements, which may target different strains in each specific bee environment. Studying the interplay between B. apis and its mobile genetic elements (MGEs) may help us better understand microbial community dynamics within the colony and the potential ramifications for the honey bee host.},
}

*CRISPR-Cas Systems/genetics
Animals
Bees/microbiology/genetics
*Evolution, Molecular
Gastrointestinal Microbiome
Phylogeny

@article {pmid40492742,
year = {2025},
author = {Edwin, NR and Duff, A and Deveautour, C and Brennan, F and Abram, F and O'Sullivan, O},
title = {Consistent microbial insights across sequencing methods in soil studies: the role of reference taxonomies.},
journal = {mSystems},
volume = {10},
number = {7},
pages = {e0105924},
pmid = {40492742},
issn = {2379-5077},
support = {2020019//Teagasc - the Agriculture and Food Development Authority/ ; SFI/16/RC/3835//Department of Agriculture, Food and the Marine, Ireland/ ; 15S655//Department of Agriculture, Food and the Marine, Ireland/ ; },
mesh = {*Soil Microbiology ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; *Bacteria/classification/genetics/isolation & purification ; Ireland ; Sequence Analysis, DNA/methods ; RNA, Ribosomal, 16S/genetics ; Grassland ; Soil/chemistry ; Phylogeny ; },
abstract = {Microbes play an important role in soil functioning, underpinning food production systems and delivering an array of essential ecosystem services. To elucidate how these microbes relate to ecosystem functions, accurate identification and classification of soil microorganisms are important. We evaluated the comparability of shotgun and amplicon sequencing approaches by profiling soil microbiota from 131 diverse temperate grassland soils across Ireland. We assessed method comparability in terms of (i) detection and classification of the most abundant phyla, (ii) their capacity to differentiate samples based on their microbial community, and (iii) their capacity to link microbial communities to measured nitrogen cycle functions. Our findings reveal that both methods offer moderately similar outcomes, providing consistent detection of major phyla, similar microbial community differentiation patterns, and largely identifying the same relationships between the phyla and nitrogen functions. The variations observed between the two methods were mostly associated with differences in the choice of reference taxonomy. Amplicon sequencing represents a cost-effective, less computationally demanding option, while shotgun sequencing provides deeper taxonomic resolution and access to the latest databases, making it suitable for detailed microbial profiling. Our study underscores the need for careful method selection based on project requirements, database availability, and financial resources.IMPORTANCEStudying the microorganisms in soil remains a challenge as soils are one of the most complex and diverse environments. Compounding these challenges is the lack of culturable representatives in soil, with over 99% of soil microorganisms yet to be cultivated in a laboratory setting. Leveraging next-generation sequencing technologies, which bypass traditional culture-dependent methods, scientists are now able to attain low-cost, high-throughput DNA sequencing that can detect even the rarest microorganisms within samples. The present study rigorously compares amplicon and shotgun sequencing techniques in profiling microbial communities across diverse temperate grassland soil samples, focusing on how different databases, classifiers, and sequencing methods influence the results. Our study underscores the crucial need for a harmonized taxonomic database that could greatly enhance comparability and accuracy in the understanding of soil microbiomes.},
}

*Soil Microbiology
*Microbiota/genetics
High-Throughput Nucleotide Sequencing/methods
*Bacteria/classification/genetics/isolation & purification
Ireland
Sequence Analysis, DNA/methods
RNA, Ribosomal, 16S/genetics
Grassland
Soil/chemistry
Phylogeny

@article {pmid40476734,
year = {2025},
author = {Marcos-Zambrano, LJ and Lacruz-Pleguezuelos, B and Aguilar-Aguilar, E and Marcos-Pasero, H and Valdés, A and Loria-Kohen, V and Cifuentes, A and Ramirez de Molina, A and Diaz-Ruiz, A and Pancaldi, V and Carrillo de Santa Pau, E},
title = {Microbiome gut community structure and functionality are associated with symptom severity in non-responsive celiac disease patients undergoing a gluten-free diet.},
journal = {mSystems},
volume = {10},
number = {7},
pages = {e0014325},
pmid = {40476734},
issn = {2379-5077},
support = {TEC-2024/BIO-167 CD3DTech-CM (ORDER 5696/2024, B.O.C.M. No. 307 12/26/2024)//Comunidad de Madrid/ ; },
mesh = {Humans ; *Celiac Disease/microbiology/diet therapy/metabolism ; *Diet, Gluten-Free ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Adult ; Middle Aged ; Cross-Sectional Studies ; Pilot Projects ; Severity of Illness Index ; Feces/microbiology ; Metabolome ; },
abstract = {UNLABELLED: Non-responsive celiac disease (NRCD) challenges clinicians due to persistent symptoms despite a gluten-free diet (GFD). We present a cross-sectional pilot study including 39 NRCD patients to describe the underlying mechanisms contributing to symptom persistence by integrating different levels of data (fecal shotgun metagenomics, mucosal integrity markers, and metabolomic profiles) and using microbial networks to unravel the community structure of the patient's microbiome. Two distinct clusters of patients were identified based on clinical and demographic variables not influenced by gluten consumption. Cluster 1, labeled "Low-grade symptoms," displayed milder symptoms and lower inflammatory markers and a fragmented microbial network characterized by high modularity and a reliance on localized hubs, suggesting a microbial community under stress but capable of maintaining limited functionality. Cluster 2, named "High-grade symptoms," exhibited more severe symptoms, elevated inflammatory markers, and a more connected but antagonistic microbial network with a greater number of keystone taxa, including taxa associated with Th17 activation and inflammation. In contrast, the control network, representing asymptomatic treated celiac disease (tCD) patients, was highly interconnected, resilient, and cooperative, with a robust structure maintained even under simulated disruptions. Metabolomic analysis revealed differential metabolites between clusters, particularly those involved in amino acid metabolism pathways and microbial-derived metabolites such as indolelactic acid and mannitol, which were associated with symptom severity. This study identifies NRCD subgroups based on the gut microbiome and metabolic signatures associated with clinical manifestations, highlighting variations in microbial network stability and metabolite profiles as contributors to symptom persistence and potential therapeutic targets.

IMPORTANCE: Celiac disease (CD) is a chronic immune-mediated systemic disorder caused by consuming gluten in genetically susceptible individuals. There is currently no cure for CD, and the most effective treatment is maintaining a strict, lifelong gluten-free diet (GFD). This nutritional therapy aims to prevent the immune reaction triggered by gluten and promote the healing of the intestinal lining, resolving the clinical, serological, and histological abnormalities within 6-12 months. However, up to 30% of patients may continue to experience symptoms or exhibit laboratory abnormalities or intestinal inflammation suggestive of active CD, despite following a GFD. This challenge, which encompasses various diagnoses, is known as nonresponsive celiac disease (NRCD). In this study, we explored the role of intestinal microbiota in causing NRCD, finding an association between the persistence of symptoms and changes in mucosal integrity biomarkers, with different gut microbiome structures among NRCD patients, indicating a significant role of the microbiome in NRCD.},
}

Humans
*Celiac Disease/microbiology/diet therapy/metabolism
*Diet, Gluten-Free
*Gastrointestinal Microbiome/physiology
Male
Female
Adult
Middle Aged
Cross-Sectional Studies
Pilot Projects
Severity of Illness Index
Feces/microbiology
Metabolome

@article {pmid40464558,
year = {2025},
author = {Ruan, Y and Zhu, T and Yang, R and Su, F and An, C and Hu, Z and Li, X and Li, Y and Chen, P and Shao, X and Qin, J and Chen, H and Chen, R},
title = {Donor-derived microbial engraftment and gut microbiota shifts associated with weight loss following fecal microbiota transplantation.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {7},
pages = {e0012025},
doi = {10.1128/aem.00120-25},
pmid = {40464558},
issn = {1098-5336},
support = {82100860//National Natural Science Foundation of China/ ; 82370864//National Natural Science Foundation of China/ ; 2019A1515110658//Natural Science Foundation of Guangdong Province/ ; 2024A04J4869//Science and Technology Program of Guangzhou/ ; },
mesh = {Humans ; *Fecal Microbiota Transplantation ; *Weight Loss ; *Gastrointestinal Microbiome ; Male ; Middle Aged ; Female ; Adult ; *Obesity/therapy/microbiology ; Feces/microbiology ; Dysbiosis/therapy ; Tissue Donors ; Bacteria/classification/genetics/isolation & purification ; Overweight/therapy/microbiology ; },
abstract = {Fecal microbiota transplantation (FMT) is a promising treatment for microbiota dysbiosis and may provide metabolic benefits for obesity. However, its mechanisms and variability in clinical outcomes remain poorly understood. This 12-week multicenter, single-arm study evaluated the efficacy of FMT for weight loss and explored the role of donor-derived microbial engraftment and functional shifts in mediating weight loss among overweight and obese individuals. Twenty-three participants (body mass index ≥24 kg/m[2]) without diabetes received three biweekly FMT sessions via a nasojejunal tube. Fecal samples from participants and donors were analyzed using metagenomic sequencing. By week 12, 52% of participants were classified as responders, achieving significant weight loss of ≥5% from baseline, with an average weight loss of 7.98 ± 2.69 kg (P < 0.001). In contrast, non-responders lost 2.90 ± 1.89 kg (P < 0.001). Responders exhibited a significantly higher proportion of donor-derived microbial strains post-FMT compared to non-responders (37.8% vs 15.2%, P = 0.020). Notably, key taxa, including Phascolarctobacterium (P = 0.034) and Acidaminococcaceae (P = 0.012), increased significantly in abundance in responders post-FMT, indicating successful microbial engraftment as a critical determinant of therapeutic success. These findings suggest that FMT is a viable intervention for weight loss in obese individuals. Successful donor-derived microbial engraftment strongly correlates with weight loss efficacy, highlighting the potential of microbiota-targeted therapies in obesity management and providing insights into the mechanisms underlying FMT outcomes.IMPORTANCEPrior research indicates that fecal microbiota transplantation (FMT) is a promising treatment for diseases related to microbiota imbalance, potentially providing metabolic benefits for obesity. However, the specific role of donor-derived microbial engraftment in driving clinical efficacy has remained unclear. In this study, we evaluated the efficacy of FMT in promoting weight loss and explored the role of donor-derived bacterial strains in this process. Our findings demonstrate that the successful engraftment of specific donor-derived taxa, such as Phascolarctobacterium and Acidaminococcaceae, is strongly associated with significant weight loss. This highlights the critical interplay between donor microbiota and recipient gut environment. These findings underscore the potential of microbiota-targeted therapies as a novel strategy for obesity management.CLINICAL TRIALSThis study is registered with the Chinese Clinical Trial Registry as ChiCTR1900024760.},
}

Humans
*Fecal Microbiota Transplantation
*Weight Loss
*Gastrointestinal Microbiome
Male
Middle Aged
Female
Adult
*Obesity/therapy/microbiology
Feces/microbiology
Dysbiosis/therapy
Tissue Donors
Bacteria/classification/genetics/isolation & purification
Overweight/therapy/microbiology

@article {pmid40461820,
year = {2025},
author = {Piccinno, G and Thompson, KN and Manghi, P and Ghazi, AR and Thomas, AM and Blanco-Míguez, A and Asnicar, F and Mladenovic, K and Pinto, F and Armanini, F and Punčochář, M and Piperni, E and Heidrich, V and Fackelmann, G and Ferrero, G and Tarallo, S and Nguyen, LH and Yan, Y and Keles, NA and Tuna, BG and Vymetalkova, V and Trompetto, M and Liska, V and Hucl, T and Vodicka, P and Bencsiková, B and Čarnogurská, M and Popovici, V and Marmorino, F and Cremolini, C and Pardini, B and Cordero, F and Song, M and Chan, AT and Derosa, L and Zitvogel, L and Huttenhower, C and Naccarati, A and Budinska, E and Segata, N},
title = {Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer.},
journal = {Nature medicine},
volume = {31},
number = {7},
pages = {2416-2429},
pmid = {40461820},
issn = {1546-170X},
support = {101045015//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 825410//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; CGCATF-2023/100036//Cancer Research UK (CRUK)/ ; CGCATF-2023/100041//Cancer Research UK (CRUK)/ ; 1OT2CA297205-01//U.S. Department of Health & Human Services | NIH | NCI | Division of Cancer Epidemiology and Genetics, National Cancer Institute (National Cancer Institute Division of Cancer Epidemiology and Genetics)/ ; OT2CA297680//U.S. Department of Health & Human Services | NIH | NCI | Division of Cancer Epidemiology and Genetics, National Cancer Institute (National Cancer Institute Division of Cancer Epidemiology and Genetics)/ ; },
mesh = {Humans ; *Colorectal Neoplasms/microbiology/pathology/genetics/diagnosis ; *Feces/microbiology ; *Metagenome/genetics ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; *Biomarkers, Tumor/genetics ; Metagenomics/methods ; Fusobacterium nucleatum/genetics ; Middle Aged ; Cohort Studies ; Aged ; Adenoma/microbiology/pathology/genetics ; Ruminococcus/genetics ; Faecalibacterium prausnitzii/genetics ; },
abstract = {Associations between the gut microbiome and colorectal cancer (CRC) have been uncovered, but larger and more diverse studies are needed to assess their potential clinical use. We expanded upon 12 metagenomic datasets of patients with CRC (n = 930), adenomas (n = 210) and healthy control individuals (n = 976; total n = 2,116) with 6 new cohorts (n = 1,625) providing granular information on cancer stage and the anatomic location of tumors. We improved CRC prediction accuracy based solely on gut metagenomics (average area under the curve = 0.85) and highlighted the contribution of 19 newly profiled species and distinct Fusobacterium nucleatum clades. Specific gut species distinguish left-sided versus right-sided CRC (area under the curve = 0.66) with an enrichment of oral-typical microbes. We identified strain-specific CRC signatures with the commensal Ruminococcus bicirculans and Faecalibacterium prausnitzii showing subclades associated with late-stage CRC. Our analysis confirms that the microbiome can be a clinical target for CRC screening and characterizes it as a biomarker for CRC progression.},
}

Humans
*Colorectal Neoplasms/microbiology/pathology/genetics/diagnosis
*Feces/microbiology
*Metagenome/genetics
*Gastrointestinal Microbiome/genetics
Female
Male
*Biomarkers, Tumor/genetics
Metagenomics/methods
Fusobacterium nucleatum/genetics
Middle Aged
Cohort Studies
Aged
Adenoma/microbiology/pathology/genetics
Ruminococcus/genetics
Faecalibacterium prausnitzii/genetics

@article {pmid40366770,
year = {2025},
author = {Baba, Y and Tsuge, D and Aoki, R},
title = {Enhancement of carbohydrate metabolism by probiotic and prebiotic intake promotes short-chain fatty acid production in the gut microbiome: a randomized, double-blind, placebo-controlled crossover trial.},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {89},
number = {8},
pages = {1191-1202},
doi = {10.1093/bbb/zbaf071},
pmid = {40366770},
issn = {1347-6947},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Fatty Acids, Volatile/biosynthesis ; *Prebiotics/administration & dosage ; Double-Blind Method ; Cross-Over Studies ; Male ; Adult ; *Probiotics/administration & dosage/pharmacology ; *Carbohydrate Metabolism/drug effects ; Female ; Feces/microbiology/chemistry ; Inulin/administration & dosage/pharmacology ; Young Adult ; Middle Aged ; },
abstract = {Short-chain fatty acids (SCFAs) are thought to be a key factor in the health benefits of prebiotics and probiotics. This study investigated the effect of Bifidobacterium animalis subsp. lactis GCL2505 and inulin (BL + IN) on fecal SCFAs and gut microbial composition and function. A placebo-controlled, randomized, double-blind, crossover study was conducted with 120 participants. Two weeks of BL + IN intake significantly increased acetate, propionate, and butyrate concentrations and Bifidobacterium abundance compared to placebo. Functional analysis of the gut metagenome showed enrichment of genes associated with carbohydrate and amino acid metabolism, suggesting an enhanced capacity for SCFA production. A responder was defined as a participant with increased fecal SCFAs after BL + IN consumption. Responder metagenomes exhibited greater enrichment of genes involved in SCFA production and carbohydrate metabolism. In conclusion, short-term BL + IN ingestion may benefit healthy adults by increasing fecal SCFAs through influencing the composition and functional activation of SCFA-associated pathways in the gut microbiome.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Fatty Acids, Volatile/biosynthesis
*Prebiotics/administration & dosage
Double-Blind Method
Cross-Over Studies
Male
Adult
*Probiotics/administration & dosage/pharmacology
*Carbohydrate Metabolism/drug effects
Female
Feces/microbiology/chemistry
Inulin/administration & dosage/pharmacology
Young Adult
Middle Aged

@article {pmid40692127,
year = {2025},
author = {Vipindas, PV and Venkatachalam, S and Jabir, T and Yang, EJ and Cho, KH and Jung, J and Lee, Y and Moon, JK and Jain, A},
title = {Distribution of Surface-Layer Prokaryotes in the Western Arctic Ocean: Responses to Pacific Water Inflow and Sea Ice Melting.},
journal = {Environmental microbiology},
volume = {27},
number = {7},
pages = {e70154},
doi = {10.1111/1462-2920.70154},
pmid = {40692127},
issn = {1462-2920},
support = {//National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Govt. of India/ ; //Korea Polar Research Institute/ ; //The Ministry of Oceans and Fisheries, Republic of Korea/ ; },
mesh = {Arctic Regions ; *Ice Cover/microbiology ; *Archaea/genetics/classification/isolation & purification ; *Seawater/microbiology ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Pacific Ocean ; Microbiota ; Metagenome ; },
abstract = {Here, we evaluated how microbial community composition and functions vary along the path of Pacific water inflow, starting from the Bering Sea via the Chukchi Sea to the central Arctic Ocean. Our findings reveal that the inflow of Pacific water and sea ice melt significantly influence the environmental settings of the western Arctic Ocean, resulting in distinct prokaryotic communities with varied distribution patterns between the open Chukchi Sea and the Ice-covered central Arctic Ocean. The heterotrophic populations reliant on phytoplankton predominated in the Bering Sea and Southern Chukchi Sea, while in the Central Arctic Ocean, chemoautotrophic bacteria and archaea contributed equally with heterotrophic populations adapted to oligotrophic conditions. Although no specific functional genes were universally enriched across the metagenome libraries of prokaryotic communities, the relative abundance of functional genes varied among oceanic sectors. The assembly processes of prokaryotic communities in the western Arctic Ocean were found to be influenced by both deterministic and stochastic factors, with deterministic processes playing a more significant role. Thus, the ongoing increases in Pacific inflow and sea ice melt could lead to the displacement of native chemoautotrophic and oligotrophic populations in the Arctic Ocean by fast-growing heterotrophic populations better adapted to elevated nutrient concentrations and temperatures.},
}

Arctic Regions
*Ice Cover/microbiology
*Archaea/genetics/classification/isolation & purification
*Seawater/microbiology
*Bacteria/genetics/classification/isolation & purification/metabolism
Pacific Ocean
Microbiota
Metagenome

@article {pmid40691525,
year = {2025},
author = {Abdelkader, A and Ferdous, NA and El-Hadidi, M and Burzykowski, T and Mysara, M},
title = {metaGEENOME: an integrated framework for differential abundance analysis of microbiome data in cross-sectional and longitudinal studies.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {189},
pmid = {40691525},
issn = {1471-2105},
mesh = {Longitudinal Studies ; *Microbiota/genetics ; *Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Cross-Sectional Studies ; Humans ; Metagenome ; },
abstract = {BACKGROUND: Detecting biomarkers is a key objective in microbiome research, often done through 16S rRNA amplicon sequencing or shotgun metagenomic analysis. A critical step in this process is differential abundance (DA) analysis, which aims to pinpoint taxa whose abundance significantly differs between groups. However, DA analysis remains challenging due to high dimensionality, compositionality, sparsity, inter-taxa correlations, uneven abundance distributions, and missing values-all which hinder our ability to model the data accurately. Despite the availability of many DA tools, balancing high statistical power with effective false discovery rate (FDR) control remains a major limitation.

RESULTS: Here, we introduce a novel approach for DA analysis that integrates counts adjusted with Trimmed Mean of M-values (CTF) normalization and Centered Log Ratio (CLR) transformation with Generalized Estimating Equation (GEE) model. We benchmarked our approach against eight widely used tools employing both simulated and real datasets in cross-sectional and longitudinal settings. While several tools (e.g. MetagenomeSeq, edgeR, DESeq2 and Lefse) achieved high sensitivity, they often failed to adequately control the FDR. In contrast, our method demonstrated high sensitivity and specificity when compared to other approaches that successfully controlled the FDR, including ALDEx2, limma-voom, ANCOM, and ANCOM-BC2.

CONCLUSIONS: Our approach effectively addresses key challenges in microbiome data analysis across both cross-sectional and longitudinal designs. Integrated into the R package metaGEENOME (https://github.com/M-Mysara/metaGEENOME), our framework provides a flexible, scalable and statistically robust solution for DA analysis, offering improved FDR control and enhanced performance for biomarker discovery in microbiome studies.},
}

Longitudinal Studies
*Microbiota/genetics
*Metagenomics/methods
RNA, Ribosomal, 16S/genetics
Cross-Sectional Studies
Humans
Metagenome

@article {pmid39966546,
year = {2025},
author = {Pietrasanta, C and Ronchi, A and Carlosama, C and Lizier, M and Silvestri, A and Fornasa, G and Melacarne, A and D'Ambrosi, F and Lutterotti, M and Carbone, E and Cetin, I and Fumagalli, M and Ferrazzi, E and Penna, G and Mosca, F and Pugni, L and Rescigno, M},
title = {Effect of prenatal antibiotics on breast milk and neonatal IgA and microbiome: a case-control translational study protocol.},
journal = {Pediatric research},
volume = {97},
number = {7},
pages = {2267-2271},
pmid = {39966546},
issn = {1530-0447},
mesh = {Humans ; Female ; *Milk, Human/immunology/chemistry ; Pregnancy ; Infant, Newborn ; *Anti-Bacterial Agents/adverse effects ; *Immunoglobulin A/metabolism ; Case-Control Studies ; Feces/microbiology/chemistry ; *Gastrointestinal Microbiome/drug effects ; Translational Research, Biomedical ; *Microbiota/drug effects ; Adult ; *Prenatal Exposure Delayed Effects ; },
abstract = {BACKGROUND: Up to 25-35% of women receive antibiotics (ABX) during pregnancy, but little is known about the consequences on a key mucosal interface such as the mammary gland, and on the development of the neonatal gut's microbiota and IgA. We hypothesize that prenatal ABX negatively affect the immune functionality of mammary gland, the composition of breast milk microbiota, the development of neonatal fecal microbiota and the abundance of neonatal fecal IgA.

METHODS: Case-control translational cohort study on women and neonates in the presence or absence (N = 41 + 41 pairs) of exposure to prenatal ABX for at least 7 consecutive days after 32 weeks of gestation.

RESULTS: We will evaluate IgA concentration in breast milk and in neonatal feces up to one year after delivery. We will also evaluate clinical parameters, neurodevelopment and the composition of the IgA-coated and uncoated fractions of breast milk and fecal microbiota by means of magnetic-activated cell sorting (MACS) coupled with shotgun metagenomics. Finally, we will measure the concentration of the chemokine CCL28 on maternal serum and breast milk, as a marker of activity of the entero-mammary pathway.

CONCLUSIONS: Our results might support a data-driven evaluation of breast milk immune function in women exposed to prenatal ABX.

IMPACT: Breast milk IgA and microbiota are critical to determine the positive effects of breastfeeding in infants. This research protocol will investigate breast milk IgA, microbiota, and the IgA[+] / IgA[-] fractions of neonatal fecal microbiota upon exposure to prenatal antibiotics. Fecal IgA and microbiota in infants exposed or not exposed to prenatal antibiotics will be analyzed up to 1 year after birth. This research will clarify the impact of prenatal antibiotics on the immune function of breast milk. This, in turn, might support the selective evaluation of breast milk IgA/microbiota in mothers exposed to prenatal antibiotics, or in donor human milk.},
}

Humans
Female
*Milk, Human/immunology/chemistry
Pregnancy
Infant, Newborn
*Anti-Bacterial Agents/adverse effects
*Immunoglobulin A/metabolism
Case-Control Studies
Feces/microbiology/chemistry
*Gastrointestinal Microbiome/drug effects
Translational Research, Biomedical
*Microbiota/drug effects
Adult
*Prenatal Exposure Delayed Effects

@article {pmid39438713,
year = {2025},
author = {Gibbons, JA and Worthington, LM and Chiu, EG and Kates, HR and Carter, RR and Nelson, R and Zhang, M and Garrett, TJ and Ho, TTB},
title = {Severe anemia in preterm infants associated with increased bacterial virulence potential and metabolic disequilibrium.},
journal = {Pediatric research},
volume = {97},
number = {7},
pages = {2415-2422},
pmid = {39438713},
issn = {1530-0447},
support = {K23 HL150300/HL/NHLBI NIH HHS/United States ; R21 HD112776/HD/NICHD NIH HHS/United States ; },
mesh = {Humans ; Infant, Premature ; Infant, Newborn ; Case-Control Studies ; Feces/microbiology ; *Gastrointestinal Microbiome ; Male ; Female ; Dysbiosis ; *Anemia/microbiology ; Virulence ; Gestational Age ; Metagenomics ; Metabolomics ; *Bacteria/pathogenicity/metabolism ; Virulence Factors/metabolism ; Metabolome ; Enterocolitis, Necrotizing ; Hematocrit ; },
abstract = {BACKGROUND: Anemia in preterm infants is associated with gut dysbiosis and necrotizing enterocolitis. Our study aimed to identify the bacterial functions and metabolites that can explain the underlying mechanisms of anemia associated disease conditions.

METHODS: We conducted a case control study in preterm infants with cases having a hematocrit ≤ 25%. The control infants were matched by birth gestational age and weight. Fecal samples were collected before, at the onset, and after the onset of anemia in cases and with matched postnatal age in controls for metagenomics and metabolomics analyzes.

RESULTS: 18 anemic and 20 control infants with fecal samples collected at 17 days, 5 weeks, and 7 weeks postnatal age were included. Virulence factor potential, decrease in beta diversity evolution, and larger changes in metabolome were associated with severe anemia. Metabolite abundances of N-acetylneuraminate and butyrobetaine were associated with virulence factor potential. Anemic group had decreased prostaglandin and lactic acid levels.

CONCLUSION: Fecal omics data showed that severe anemia is associated with a pro-inflammatory gut microbiota with more virulent and less commensal anaerobic bacterial activities. Future studies can examine the link between anemia-associated dysbiosis and clinical outcomes and predict an infant-specific hematocrit threshold that negatively affects clinical outcomes.

IMPACT: Severe anemia in preterm infants contributes to a pro-inflammatory gut with greater bacterial virulence and less commensal bacterial activities. The multiomics approach using non-invasive fecal biospecimens identified functional and metabolic changes in the gut microbiota and these mechanistic changes are plausible explanations for anemia-associated disease conditions in preterm infants. Our findings identified biological changes of the gut environment in severely anemic preterm infants that can offer guidance for clinical management.},
}

Humans
Infant, Premature
Infant, Newborn
Case-Control Studies
Feces/microbiology
*Gastrointestinal Microbiome
Male
Female
Dysbiosis
*Anemia/microbiology
Virulence
Gestational Age
Metagenomics
Metabolomics
*Bacteria/pathogenicity/metabolism
Virulence Factors/metabolism
Metabolome
Enterocolitis, Necrotizing
Hematocrit

@article {pmid39433961,
year = {2025},
author = {Li, J and Shen, N and He, W and Pan, Y and Wu, J and Zhao, R and Mo, X and Li, Y},
title = {Gut microbiome impact on childhood allergic rhinitis and house dust mite IgE responses.},
journal = {Pediatric research},
volume = {97},
number = {7},
pages = {2405-2414},
pmid = {39433961},
issn = {1530-0447},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Immunoglobulin E/blood/immunology ; *Rhinitis, Allergic/immunology/microbiology ; Humans ; *Pyroglyphidae/immunology ; Child ; Female ; Mice ; Male ; Child, Preschool ; Feces/microbiology ; Cytokines/blood ; Case-Control Studies ; Spleen/immunology ; },
abstract = {BACKGROUND: The correlation between the gut microbiota and airway inflammation in childhood allergic rhinitis (AR), particularly concerning allergen exposure, remains insufficiently explored. This study aimed to link gut microbiota changes with house dust mite (HDM)-specific IgE responses in pediatric AR.

METHODS: Using metagenomic shotgun sequencing, we compared the fecal microbiota of 60 children with HDM-AR to 48 healthy controls (HC), analyzing the link to IgE reactions. We examined the effects of oral Escherichia (E.) fergusonii treatment in mice sensitized with ovalbumin and HDM on allergic symptoms, mucosal cell infiltration, Th1/Th2/Tregs balance in the spleen, serum cytokine levels, and E. fergusonii presence in feces.

RESULTS: Children with HDM-AR have a less diverse gut microbiome and lower levels of E. fergusonii compared to controls, with a negative correlation between E. fergusonii abundance and HDM-specific IgE levels. In mice sensitized with OVA and HDM, oral administration of E. fergusonii improved allergic symptoms, reduced nasal eosinophils/mast cells infiltration and adjusted Th cell populations towards a non-allergic profile in splenic lymphocytes with exception of IFN-γ change in serum.

CONCLUSION: These findings underline the potential of targeting gut microbiota, particularly E. fergusonii, in managing childhood HDM-AR, suggesting a promising approach for future interventions.

IMPACT: The composition and distribution of gut microbiota in children with HDM-AR are significant changed. The abundance of Escherichia genus is decreased in HDM-AR children. HDM-specific IgE levels are strongly negatively associated with E. fergusonii abundance. Oral administration of E. fergusonii effectively suppresses allergic responses in murine model. These findings offer novel insights into the diagnosis and treatment of HDM-AR, which suggested that E. fergusonii holds promise as a potential therapeutic avenue for managing HDM-AR.},
}

Animals
*Gastrointestinal Microbiome
*Immunoglobulin E/blood/immunology
*Rhinitis, Allergic/immunology/microbiology
Humans
*Pyroglyphidae/immunology
Child
Female
Mice
Male
Child, Preschool
Feces/microbiology
Cytokines/blood
Case-Control Studies
Spleen/immunology

@article {pmid40691449,
year = {2025},
author = {Vázquez-Castellanos, JF and Maciel, LF and Wauters, L and Gregory, A and Van Oudenhove, L and Geboers, K and Verbeke, K and Smokvina, T and Tack, J and Vanuytsel, T and Derrien, M and Raes, J},
title = {Probiotic-mediated modulation of gut microbiome in students exposed to academic stress: a randomized controlled trial.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {140},
pmid = {40691449},
issn = {2055-5008},
mesh = {Humans ; *Probiotics/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; *Stress, Psychological/microbiology ; *Students/psychology ; Male ; Female ; *Lacticaseibacillus rhamnosus/physiology ; RNA, Ribosomal, 16S/genetics ; Young Adult ; Adult ; Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Anxiety ; Metagenomics ; },
abstract = {Probiotics have been widely tested for their effect on mental well-being, albeit with heterogeneous outcomes. Direct and indirect effects through the gut microbiome might lie at the basis of these observations. Here, in a post-hoc analysis, we assessed the effect of 4-week consumption of a probiotic candidate strain on the gut microbiome in students exposed to academic stress. Healthy students were randomized to consume a fermented milk product with Lacticaseibacillus rhamnosus CNCM I-3690 (N = 39) or an acidified non-fermented milk product (N = 40) twice daily for 4 weeks before academic exams. The gut microbiome was analysed by Quantitative Microbiome Profiling based on 16S rRNA gene amplicon and shotgun metagenomic sequencing. Stress and anxiety were assessed using both objective and self-reported markers. Changes of alpha-diversity markers and community shifts from baseline (beta diversity) were lower in L. rhamnosus treated individuals over controls, suggesting lower overall changes of gut microbiota during psychological stress in the Probiotic group. The intake of L. rhamnosus CNCM I-3690 induced differential abundance of some species, such as the maintenance of the quantitative abundance of Ruminococcus bicirculans, and co-varied with species, which differed according to visits (i.e., stress level), suggesting a potential beneficial effect of the strain before the highest increase of stress level. The higher quantitative abundance of F. prausnitzii induced by the probiotic intake was associated with lowered self-reported anxiety levels before the exam. Functional analysis revealed minor changes upon intake of the probiotic strain. Taken together, using a quantitative framework, we found that L. rhamnosus CNCM I-3690 has a potential effect on gut microbiome response to stress, although further studies are needed to better understand the precise interaction.},
}

Humans
*Probiotics/administration & dosage
*Gastrointestinal Microbiome/drug effects
*Stress, Psychological/microbiology
*Students/psychology
Male
Female
*Lacticaseibacillus rhamnosus/physiology
RNA, Ribosomal, 16S/genetics
Young Adult
Adult
Feces/microbiology
*Bacteria/classification/genetics/isolation & purification
Anxiety
Metagenomics

@article {pmid40691217,
year = {2025},
author = {Leung, HKM and Lo, EKK and Chen, C and Zhang, F and Felicianna, and Ismaiah, MJ and El-Nezami, H},
title = {Theabrownin combined with zearalenone suppresses colitis-associated colorectal cancer by inhibiting PI3K/AKT pathway and enhancing microbial propionate production.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {26386},
pmid = {40691217},
issn = {2045-2322},
mesh = {*Zearalenone/pharmacology/administration & dosage ; Animals ; Mice ; *Proto-Oncogene Proteins c-akt/metabolism ; *Phosphatidylinositol 3-Kinases/metabolism ; Gastrointestinal Microbiome/drug effects ; *Propionates/metabolism ; Signal Transduction/drug effects ; *Colorectal Neoplasms/drug therapy/etiology ; *Colitis-Associated Neoplasms/drug therapy/metabolism/pathology ; Male ; Cytokines/metabolism ; Fluorouracil/pharmacology ; *Colitis/complications ; Mice, Inbred C57BL ; },
abstract = {Colorectal cancer (CRC) is both a leading cause of cancer-related mortality and one of the most frequently diagnosed cancers. Previous studies have shown that zearalenone and theabrownin each exert anti-CRC effects. Here, we aimed to evaluate the anti-tumor properties of theabrownin and zearalenone mixture (TZ) and to assess whether supplementing TZ with 5-FU, a commonly used chemotherapeutic drug, could further suppress CRC tumorigenesis. Our results revealed that TZ significantly attenuated AOM/DSS-induced colorectal tumorigenesis. TZ improved survival rate, reduced tumor count, preserved colon length, and mitigated colonic inflammation in AOM/DSS mice. In addition, the concentration of pro-inflammatory cytokines IL-6, TNF-α and IL-17 A/F and proliferative PI3K/AKT were significantly reduced. Metagenomic analyses revealed that TZ modulated the gut microbiota and mycobiota composition and increased the fecal acetate and propionate levels. Furthermore, the enrichment of the bacterial Desulfovibrionaceae bacterium LT0009, Helicobacter sp. MIT 03-1616 and fungal Xylariaceae sp. FL0594 was associated with the reduction of tumor multiplicity and pro-inflammatory cytokines. No additional benefits were observed with combining TZ with 5-FU. Taken together, TZ presented remarkable inhibitory effects on colorectal tumorigenesis, indicating its potential as a novel therapeutic candidate for CRC.},
}

*Zearalenone/pharmacology/administration & dosage
Animals
Mice
*Proto-Oncogene Proteins c-akt/metabolism
*Phosphatidylinositol 3-Kinases/metabolism
Gastrointestinal Microbiome/drug effects
*Propionates/metabolism
Signal Transduction/drug effects
*Colorectal Neoplasms/drug therapy/etiology
*Colitis-Associated Neoplasms/drug therapy/metabolism/pathology
Male
Cytokines/metabolism
Fluorouracil/pharmacology
*Colitis/complications
Mice, Inbred C57BL

@article {pmid40686474,
year = {2025},
author = {Lledós, M and Prats-Sánchez, L and Muiño, E and Cullell, N and Llucià-Carol, L and Cárcel-Márquez, J and Gallego-Fabrega, C and Martín-Campos, JM and Marín, R and Aguilera-Simón, A and Guasch-Jiménez, M and Ezcurra-Díaz, G and Camps-Renom, P and Del Mar Freijo, M and Martí-Fàbregas, J and Fernández-Cadenas, I},
title = {Influence of the Gut Microbiota on Acute Ischemic Stroke Functional Outcomes at Three Months.},
journal = {European journal of neurology},
volume = {32},
number = {7},
pages = {e70265},
doi = {10.1111/ene.70265},
pmid = {40686474},
issn = {1468-1331},
support = {RD21/0006/0006//RICORS-ICTUS/ ; AC19/00106//ERA-Net NEURON/ ; CD20/00043//Instituto de Salud Carlos III/ ; FI19/00309//Instituto de Salud Carlos III/ ; PI18/01338//Instituto de Salud Carlos III/ ; PI20/00925//Instituto de Salud Carlos III/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Ischemic Stroke/microbiology/physiopathology ; Male ; Female ; Aged ; Middle Aged ; *Recovery of Function/physiology ; Genome-Wide Association Study ; },
abstract = {BACKGROUND: Functional recovery from ischemic stroke (IS), the main cause of adult disability worldwide, is influenced by many factors, and a portion of interindividual variability remains unexplained.

METHODS: Observational study in a tertiary stroke centre of patients with IS analyzed using shotgun metagenomic sequencing (January 2020-March 2022). Functional outcomes were assessed according to modified Rankin Scale (mRS) scores 3-months post-IS, considering 0-2 favorable and 3-6 unfavorable. The causal relationship between several bacteria and post-IS outcomes was explored via two-sample Mendelian randomization (MR) analyses using Genome-Wide Association Analysis (GWAS) summary statistics.

RESULTS: Comparing 128 patients with favorable and unfavorable post-IS functional outcomes, β-diversity analysis showed a separation in microbial structure, and α-diversity measures revealed greater bacterial richness in the favorable outcomes group. Taxonomic profiling of the samples showed that a greater abundance of pathogenic bacteria (e.g., Pseudomonas, Finegoldia, Porphyromonas) was associated with an unfavorable outcome. Functional profiling of the samples revealed differences in the ethylbenzene degradation pathway and in 16S rRNA (uracil1498-N3)-methyltransferase. MR confirmed increased pyruvate levels to be causally associated with post-IS favorable outcomes (β = -0.50, 95% CI: -0.91, -0.10).

CONCLUSIONS: Our study points to gut microbiota differences in patients with unfavorable versus favorable 3-month post-IS outcomes. Patients with unfavorable outcomes presented gut microbiota dysbiosis and alterations in multiple metabolic pathways.

TRIAL REGISTRATION: This study was registered on 3 October 2021 with https://clinicaltrials.gov. Access number: NCT04795687.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Ischemic Stroke/microbiology/physiopathology
Male
Female
Aged
Middle Aged
*Recovery of Function/physiology
Genome-Wide Association Study

@article {pmid40685922,
year = {2025},
author = {Chen, QY and Shao, MM and Dong, SF and Shi, HZ and Yi, FS},
title = {Metagenomic and Metabolomic Profiling Reveals the Impact of High-Fat Diet on Malignant Pleural Effusion.},
journal = {Thoracic cancer},
volume = {16},
number = {14},
pages = {e70126},
doi = {10.1111/1759-7714.70126},
pmid = {40685922},
issn = {1759-7714},
support = {7232066//Natural Science Foundation of Beijing Municipality/ ; 82200111//National Natural Science Foundation of China/ ; 048//Beijing Scholars Program/ ; QML20230303//Beijing Hospitals Authority Youth Program/ ; Ggyfz202314//Reform and Development Program of Beijing Institute of Respiratory Medicine/ ; Ggyfz202330//Reform and Development Program of Beijing Institute of Respiratory Medicine/ ; Ggyfz202416//Reform and Development Program of Beijing Institute of Respiratory Medicine/ ; },
mesh = {Animals ; Mice ; *Diet, High-Fat/adverse effects ; *Metabolomics/methods ; *Metagenomics/methods ; *Pleural Effusion, Malignant/etiology/metabolism/pathology ; Male ; Gastrointestinal Microbiome ; Humans ; *Metabolome ; Mice, Inbred C57BL ; },
abstract = {BACKGROUND: Malignant pleural effusion (MPE) is a common complication in the advanced stage of cancer. High-Fat Diet (HFD)-induced obesity has become a common metabolic background in cancer patients. Recent studies have demonstrated that HFD induces gut dysbiosis, resulting in alterations in metabolites and immune responses. However, its role in MPE remains unclear.

METHODS: We established an MPE mouse model under both normal chow and HFD conditions. Metagenomic sequencing of fecal samples and untargeted metabolomics of plasma were performed to assess alterations in gut microbiota and systemic metabolites, respectively. Bioinformatic and statistical analyses were conducted to identify significant microbial taxa and metabolic pathways.

RESULTS: HFD-fed mice exhibited increased pleural effusion. Metagenome data of the intestinal microbiome and metabolome profiles of plasma metabolites revealed key taxa-Akkermansiaceae, Parabacteroides, and Muribaculaceae-as well as significant metabolic pathways involved in sphingolipid metabolism, glycerophospholipid metabolism, and steroid hormone biosynthesis.

CONCLUSION: These findings suggest that HFD may accelerate the MPE progression through modulation of gut microbiota and plasma metabolites, providing new strategies for prevention and treatment.},
}

Animals
Mice
*Diet, High-Fat/adverse effects
*Metabolomics/methods
*Metagenomics/methods
*Pleural Effusion, Malignant/etiology/metabolism/pathology
Male
Gastrointestinal Microbiome
Humans
*Metabolome
Mice, Inbred C57BL

@article {pmid40685618,
year = {2025},
author = {Morsy, Y and Walberg, Å and Wawrzyniak, P and Hubeli, B and Truscello, L and Mamie, C and Niechcial, A and Gueguen, E and Manzini, R and Gottier, C and Lang, S and Scharl, S and Blümel, S and Biedermann, L and Rogler, G and Turina, M and Ramser, M and Petrowsky, H and Arnold, IC and Zeissig, S and Zamboni, N and Egli, A and Niess, JH and Hruz, P and Knuth, A and Fritsch, R and Manz, MG and Wawrzyniak, M and Scharl, M},
title = {Blood-borne immune cells carry low biomass DNA remnants of microbes in patients with colorectal cancer or inflammatory bowel disease.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2530157},
doi = {10.1080/19490976.2025.2530157},
pmid = {40685618},
issn = {1949-0984},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/immunology/blood ; *Inflammatory Bowel Diseases/microbiology/immunology/blood ; *Leukocytes, Mononuclear/microbiology/immunology ; *Gastrointestinal Microbiome ; *Bacteria/genetics/classification/isolation & purification ; Male ; Female ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; *DNA, Bacterial/genetics ; Metagenomics ; Adult ; Bacterial Translocation ; Aged ; },
abstract = {The involvement of the intestinal microbiome in the pathogenesis of inflammatory bowel disease (IBD) and colorectal cancer (CRC), is well-established. Bacteria interact with immune cells at sites of intestinal inflammation, but also in the CRC tumor microenvironment. We hypothesized that bacterial remnants translocate within peripheral blood mononuclear cells (PBMCs) into the circulation and thus explored the composition of the detectable microbiome in PBMCs of patients with CRC or IBD compared to healthy controls. The PBMC microbiome profiles partially align with the tumor-derived or intestinal tissue-derived microbiome signatures obtained from the same patients with CRC or IBD, respectively. Our metagenomics data, supported by 16S-rRNA-FISH-Flow, imaging flow cytometry and species-specific qPCR, revealed the presence of translocated bacterial genetic sequences in the patients with CRC and IBD. Thus, our data suggest that in patients with intestinal barrier leakage, there is the potential for the translocation of bacterial remnants into the circulation via PBMCs.},
}

Humans
*Colorectal Neoplasms/microbiology/immunology/blood
*Inflammatory Bowel Diseases/microbiology/immunology/blood
*Leukocytes, Mononuclear/microbiology/immunology
*Gastrointestinal Microbiome
*Bacteria/genetics/classification/isolation & purification
Male
Female
Middle Aged
RNA, Ribosomal, 16S/genetics
*DNA, Bacterial/genetics
Metagenomics
Adult
Bacterial Translocation
Aged

@article {pmid40684088,
year = {2025},
author = {Kreisinger, J and Kaňková, Š and Dlouhá, D and Ullmann, J and Nouzová, K and Hrbáčková, H and Schmiedová, L and Takács, L},
title = {Associations between psychological or biological stress indicators and gut microbiota in pregnant women - findings from a prospective longitudinal study.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {442},
pmid = {40684088},
issn = {1471-2180},
support = {21-23288S//Grantová Agentura České Republiky,Czechia/ ; 21-23288S//Grantová Agentura České Republiky,Czechia/ ; 21-23288S//Grantová Agentura České Republiky,Czechia/ ; 21-23288S//Grantová Agentura České Republiky,Czechia/ ; 21-23288S//Grantová Agentura České Republiky,Czechia/ ; 21-23288S//Grantová Agentura České Republiky,Czechia/ ; 21-23288S//Grantová Agentura České Republiky,Czechia/ ; 21-23288S//Grantová Agentura České Republiky,Czechia/ ; CZ.02.01.01/00/22_008/0004597//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; CZ.02.01.01/00/22_008/0004597//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; },
mesh = {Humans ; Female ; Pregnancy ; *Gastrointestinal Microbiome ; Longitudinal Studies ; Prospective Studies ; Adult ; RNA, Ribosomal, 16S/genetics ; Anxiety/microbiology ; *Stress, Psychological/microbiology ; Depression/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Hydrocortisone/blood ; Young Adult ; Surveys and Questionnaires ; Pregnant People/psychology ; Postpartum Period ; },
abstract = {BACKGROUND: The perinatal period has been linked with higher vulnerability to stress and symptoms of depression and anxiety, as well as with dynamic changes in the composition of maternal gut microbiota. While recent studies indicated significant associations between stress, depression, or anxiety, and alterations in gut microbiota in pregnant women, research in this avenue is still emerging, with existing studies often being limited by small sample sizes.

METHOD: We conducted a prospective longitudinal study of 171 women, collecting gut microbiota samples in each trimester of pregnancy and in the early postpartum, questionnaire data (perceived stress via the Perceived Stress Scale, symptoms of depression via the Edinburgh Postnatal Depression Scale, and anxiety via the 6-item State-Trait Anxiety Inventory) twice in each trimester and twice in the early postpartum period, and blood samples for cortisol levels analysis in the first and third pregnancy trimesters. Gut microbiota samples were analyzed by amplicon sequencing of 16S rRNA gene.

RESULTS: Perceived stress and symptoms of depression and anxiety showed moderate temporal changes and a high consistency at the individual level over the study period. Cortisol levels rose significantly from the first to the third trimester. There were significant temporal changes in microbiota composition between the first and second trimesters, and between the first and third trimesters. After controlling for false positive findings due to multiple testing, we found no significant associations between stress-related variables (perceived stress, cortisol levels, symptoms of depression and anxiety) and gut microbiota diversity, microbial community composition, or relative abundances of individual bacterial taxa.

CONCLUSIONS: The present study results contradict previous research that indicated significant associations between emotions and gut microbiota in the perinatal period. Although we cannot provide an ultimate explanation for this discrepancy, we propose it can lie in insufficient control for false positives in the differential abundance analyses in most previous studies.},
}

Humans
Female
Pregnancy
*Gastrointestinal Microbiome
Longitudinal Studies
Prospective Studies
Adult
RNA, Ribosomal, 16S/genetics
Anxiety/microbiology
*Stress, Psychological/microbiology
Depression/microbiology
*Bacteria/classification/genetics/isolation & purification
Hydrocortisone/blood
Young Adult
Surveys and Questionnaires
Pregnant People/psychology
Postpartum Period

@article {pmid40467356,
year = {2025},
author = {Messadi, A and Sayhi, S and Ghedira, K and Zaouaoui, C and Arfaoui, B and Khouikhi, S and Rebai, M and Guediche, NEH and Abdelhafidh, N and Louzir, B and Faida, A},
title = {Microbial diversity investigation using 16S metagenomics in Tunisian patients with systemic lupus erythematosus.},
journal = {Revista Argentina de microbiologia},
volume = {57},
number = {3},
pages = {275-287},
doi = {10.1016/j.ram.2025.04.002},
pmid = {40467356},
issn = {0325-7541},
mesh = {Humans ; *Lupus Erythematosus, Systemic/microbiology ; Tunisia ; Female ; *Metagenomics ; Case-Control Studies ; Adult ; Male ; Middle Aged ; *RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; Dysbiosis/microbiology ; Young Adult ; Bacteria/classification/isolation & purification/genetics ; },
abstract = {Systemic lupus erythematosus (SLE) is a multisystemic autoimmune disease associated with significant morbidity and mortality. It is characterized by a loss of self-immune tolerance and autoantibody production, leading to multiple organ damage. Emerging investigations have confirmed the role of gut microbiota dysbiosis in patients with SLE, although the underlying mechanisms remain unclear to date. In this study, we aim to investigate the bacterial profile of SLE including phylum/class/genus relative abundance and diversity, to compare them with healthy controls and to study the correlation of relative abundance of different patterns with clinical/biological parameters. In this case-control study, the bacterial profile was investigated in 7 SLE patients and 7 healthy controls using 16S metagenomics clustering. The present study reported a low abundance of the class Bacilli (0.58% in SLE vs 1.26% in the controls), the genus Lactobacillus (0.43% vs 0.74%), as well as a higher abundance of the genera Gammaproteobacteria (2.37% vs 0.77%) and Escherichia-Shigella (2.04% vs 0.51%) in SLE samples compared to the controls (p<0.05). We also found an association between the class Betaproteobacteria (4.42% vs 1.57%) and the genus Faecalibacterium (11.34% vs 3.35%) and renal manifestations (p<0.05). The phylum Actinobacteria (0.21% vs 3.8%, p=0.036) and the genus Bifidobacterium levels were lower in active SLE compared to the healthy controls. This study is the first report on the gut microbiota of SLE and the first case-control study in Tunisia and North Africa. We obtained a particular profile of bacterial gut microbiota for the SLE group. We found a specific clustering when compared to the healthy controls.},
}

Humans
*Lupus Erythematosus, Systemic/microbiology
Tunisia
Female
*Metagenomics
Case-Control Studies
Adult
Male
Middle Aged
*RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome
Dysbiosis/microbiology
Young Adult
Bacteria/classification/isolation & purification/genetics

@article {pmid39426464,
year = {2025},
author = {Tang, Y and Liu, X and Zhu, S and Jia, M and Liu, JX and Sun, HZ},
title = {New insights into the enteric methane production based on the archaeal genome atlas of ruminant gastrointestinal tract.},
journal = {Journal of advanced research},
volume = {74},
number = {},
pages = {13-24},
doi = {10.1016/j.jare.2024.09.016},
pmid = {39426464},
issn = {2090-1224},
mesh = {Animals ; *Methane/biosynthesis/metabolism ; *Archaea/genetics/metabolism/classification ; Cattle ; *Genome, Archaeal/genetics ; *Gastrointestinal Microbiome/genetics ; Rumen/microbiology ; Phylogeny ; *Ruminants/microbiology ; *Gastrointestinal Tract/microbiology/metabolism ; Metagenomics/methods ; },
abstract = {INTRODUCTION: As one of the important components of ruminant gastrointestinal tract (GIT) microbiome, archaea are involved in many biological processes, especially methanogenesis. In spite of being a well-recognised member of the mammalian gut microbiome, it remains poorly characterized, partly due to the lack of a unified reference genome catalog.

OBJECTIVES: This study aimed to construct a unified genome atlas that captures the wider diversity in archaea and is thus more appropriate for functional and taxonomic exploration of ruminant GIT archaea.

METHODS: We collected archaeal genomes from public sources and new data of this study. We performed phylogenetic and functional genomics analysis, prophage identification based on the genomes. Using collected genomes as a reference, we conducted metagenomic and metatranscriptomic analysis on rumen fluid samples from 18 dairy cows, and investigated the correlation between rumen archaeal communities and methane (CH4) production profiles.

RESULTS: We constructed the ruminant GIT archaeal genomes (RGAG) by compiling 405 strain-level (160 species) non-redundant archaeal genomes from more than 10 ruminant species. Investigating the functional heterogeneity and methanogenic structure within RGAG revealed that it possessed 1,124 (99.5%) unknown microbial biosynthetic gene clusters. A survey of RGAG-borne prophages identified 63 prophages with 122 host-beneficial genes and 18 auxiliary metabolic genes. The pipeline for both metagenomics and metatranscriptomics generated in the study revealed the roles of archaeal genomes under-assessed in general multi-omics analysis. The highly expressed genus Methanosphaera was negatively correlated with CH4 production at the RNA level.

CONCLUSION: A unified genome atlas of ruminant GIT archaea is constructed in the study. Our analyses revealed the advantages of metatranscriptomics over metagenomics in studying rumen archaeal communities and further demonstrated that the multifaceted functions of ruminant archaea remain undiscovered. Differences in rumen archaeal community structure among cattle with different CH4 production profiles may reflect the balance between rumen hydrogen production and methanogenesis. Our work provides a new resource for interrogating archaeal functions in the ruminant GIT and potential targets for future CH4 reduction.},
}

Animals
*Methane/biosynthesis/metabolism
*Archaea/genetics/metabolism/classification
Cattle
*Genome, Archaeal/genetics
*Gastrointestinal Microbiome/genetics
Rumen/microbiology
Phylogeny
*Ruminants/microbiology
*Gastrointestinal Tract/microbiology/metabolism
Metagenomics/methods

@article {pmid40683926,
year = {2025},
author = {Zafeiropoulou, K and Voermans, B and Ngo, H and Moreno, J and Lee, D and Derikx, JPM and Luyer, M and Zwinderman, AH and Nieuwdorp, M and de Goffau, M and de Jonge, WJ and Levin, E},
title = {Application of image guided analyses to monitor fecal microbial composition and diversity in a human cohort.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {26237},
pmid = {40683926},
issn = {2045-2322},
support = {09150182010020//Amsterdam University Medical Centers/ ; 101141346/ERC_/European Research Council/International ; },
mesh = {Humans ; *Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Female ; Male ; Cohort Studies ; Adult ; Smartphone ; *Bacteria/genetics/classification ; Metagenomics/methods ; Middle Aged ; },
abstract = {The critical role of gut microbiota in human health and disease has been increasingly illustrated over the past decades, with a significant amount of research demonstrating an unmet need for self-monitor of the fecal microbial composition in an easily-accessible, rapid-time manner. In this study, we employed a tool for Smartphone Microbiome Evaluation and Analysis in Rapid-time (SMEAR) that uses images of fecal smears to predict microbial compositional characteristics in a human cohort. A subset of human fecal samples was randomly retrieved from the second wave of data collection in the Healthy Life in an Urban Setting (HELIUS) study cohort. Per sample, 16S rRNA gene sequencing data was generated in addition to an image of a fecal smear, spread on a standard A4 paper. Metagenomics-paired pictures were used to validate a computer vision-based technology to classify whether the sample is of low or high relative abundance of the 50 most abundant genera, and α-diversity (Shannon-index). In total, 888 fecal samples were used as an application of the SMEAR technology. SMEAR gave accurate predictions whether a fecal sample is of low or high relative abundance of Sporobacter, Oscillibacter and Intestinimonas (very good performance, AUC > 0.8, p-value < 0.001, for all models), as well as Neglecta, Megasphaera, Lachnospira, Methanobrevibacter, Harryflintia, Roseburia, and Dialister (good performance, AUC > 0.75, p-value < 0.001, for all models). Likewise, SMEAR could classify whether a fecal sample was of low or high α-diversity (AUC = 0.83, p-value < 0.001). Our study demonstrates that SMEAR robustly predicts microbial composition and diversity from digital images of fecal smears in a human cohort. These findings establish SMEAR as a new benchmark for rapid, cost-effective microbiome diagnostics and pave the way for its direct application in research settings and clinical validation.},
}